Contacts of the helix formed by residues 74 - 99 (chain A) in PDB entry 1L8A
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 74 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLY* 1.3 67.6 - - - -
75A LEU* 1.3 63.3 + - - +
76A GLU* 3.3 16.7 + - - +
77A LEU* 3.1 37.0 + - + +
78A GLU* 2.9 24.7 + - - +
446A GLU* 4.5 7.1 + - - -
450A TYR* 3.1 25.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 3.6 34.1 - - + -
73A GLY 3.1 7.9 + - - +
74A ASN* 1.3 71.5 + - - +
76A GLU* 1.3 58.3 + - - +
78A GLU* 3.5 6.4 + - - +
79A ARG* 3.1 27.7 + - - +
82A ARG* 4.9 2.6 + - - -
366A PRO* 3.7 31.0 - - + -
367A LYS* 4.2 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 3.3 15.2 + - - +
75A LEU* 1.3 75.6 - - - +
77A LEU* 1.3 76.3 + - - +
79A ARG* 3.3 7.5 + - - +
80A ARG* 3.0 59.0 + - + +
446A GLU* 4.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 3.1 26.2 + - + +
76A GLU* 1.3 82.6 + - - +
78A GLU* 1.3 64.6 + - - +
80A ARG* 3.2 33.0 + - - +
81A ILE* 3.1 23.1 + - + +
446A GLU* 3.8 24.5 - - + +
447A GLU* 3.6 28.3 - - + +
450A TYR* 3.4 42.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TYR* 2.6 32.4 + - - -
73A GLY* 3.5 1.7 - - - -
74A ASN 2.9 19.0 + - - +
75A LEU* 3.7 9.1 - - + +
77A LEU* 1.3 75.4 - - - +
79A ARG* 1.3 60.0 + - - +
81A ILE* 3.2 8.5 + - - +
82A ARG* 2.8 42.3 + - - +
118A ASP* 3.7 2.3 - - - +
122A ASN* 3.5 19.3 + - - +
123A HIS* 2.9 20.8 + - - -
366A PRO* 5.1 1.0 - - - +
450A TYR* 2.5 40.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU 3.1 18.0 + - - +
76A GLU* 3.6 7.4 - - - +
77A LEU 3.3 0.4 - - - -
78A GLU* 1.3 77.6 - - - +
80A ARG* 1.3 59.2 + - - +
82A ARG* 3.5 27.0 - - - +
83A SER* 2.8 42.8 + - - -
394A TYR* 5.8 0.4 + - - -
423A ARG* 3.1 38.8 + - - +
424A PHE* 3.5 27.5 + - - -
425A ASN* 2.8 31.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 3.0 53.5 + - + +
77A LEU* 3.3 22.6 - - - +
78A GLU 3.2 0.4 - - - -
79A ARG* 1.3 79.9 - - + +
81A ILE* 1.3 60.8 + - - +
83A SER* 3.6 5.4 + - - -
84A ALA* 3.4 15.1 + - - +
441A PHE* 3.8 12.1 - - + -
446A GLU* 3.4 32.3 + - - +
447A GLU* 2.6 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU 3.1 16.6 + - - +
78A GLU* 3.2 7.6 + - - +
80A ARG* 1.3 75.4 - - - +
82A ARG* 1.3 64.3 + - - +
84A ALA* 3.2 5.4 + - - +
85A ILE* 3.1 33.6 + - + +
118A ASP* 5.0 3.1 - - - +
122A ASN* 5.5 5.2 - - - +
150A ARG* 4.9 3.1 - - - +
153A LEU* 5.5 0.9 - - + -
441A PHE* 4.0 14.6 - - + -
447A GLU* 3.7 39.0 - - + +
450A TYR* 3.7 31.2 - - + -
451A LEU* 3.9 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU 4.9 2.6 + - - -
78A GLU* 2.8 34.6 + - - +
79A ARG* 3.5 32.6 - - - +
81A ILE* 1.3 74.8 - - - +
83A SER* 1.3 56.9 + - - +
85A ILE* 3.3 9.2 + - + +
86A ARG* 2.9 49.1 + - + +
114A ALA* 4.3 4.3 - - + -
115A THR* 3.5 38.1 + - - +
118A ASP* 2.5 58.8 + - + +
119A VAL* 5.8 1.0 - - - +
364A HIS 5.7 0.2 + - - -
366A PRO* 4.2 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 2.8 36.9 + - - -
80A ARG* 3.9 6.7 - - - -
81A ILE 3.2 0.2 - - - -
82A ARG* 1.3 69.8 - - - +
84A ALA* 1.3 61.5 + - - +
86A ARG* 3.2 11.4 + - - +
87A TRP* 2.9 30.0 + - - +
424A PHE* 3.0 40.6 + - - +
425A ASN 5.2 2.0 - - - -
426A VAL* 4.2 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG 3.4 3.7 + - - +
81A ILE 3.2 6.8 + - - +
83A SER* 1.3 78.4 - - - +
85A ILE* 1.3 58.1 + - - +
87A TRP* 3.3 1.7 + - - +
88A ASN* 2.9 34.7 + - - -
153A LEU* 4.0 8.1 - - + -
426A VAL* 5.4 0.4 - - - -
427A PRO* 5.6 3.3 - - + +
439A ILE* 4.2 26.7 - - + -
441A PHE* 3.3 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 3.1 26.3 + - + +
82A ARG* 3.6 8.5 - - + +
84A ALA* 1.3 73.7 - - - +
86A ARG* 1.3 65.7 + - - +
89A ALA* 3.0 21.5 + - - +
110A PHE* 4.0 17.9 - - + -
118A ASP* 4.3 8.7 - - - +
146A GLY 3.7 22.0 - - - +
149A ALA* 3.2 10.7 - - + +
150A ARG* 3.8 44.4 - - + +
153A LEU* 3.5 21.8 - - + -
451A LEU* 5.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG* 2.9 35.9 + - - +
83A SER* 3.4 9.8 + - - +
85A ILE* 1.3 77.7 - - - +
87A TRP* 1.3 61.9 + - - +
89A ALA* 3.4 2.6 + - - +
90A ILE* 3.1 31.5 + - + +
110A PHE* 4.4 4.9 - - + -
111A GLN* 3.0 57.3 + - - +
114A ALA* 3.6 21.6 - - + +
115A THR* 3.0 27.1 + - - +
364A HIS* 5.1 0.6 - - - -
394A TYR* 3.7 20.8 - - - -
420A ILE* 5.5 0.9 - - + -
424A PHE* 3.6 39.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER 2.9 16.6 + - - +
84A ALA 3.6 3.4 - - - +
86A ARG* 1.3 76.1 - - - +
88A ASN* 1.3 62.4 + - - +
90A ILE* 3.1 4.9 + - - +
91A MET* 2.8 59.5 + - + +
417A VAL* 3.5 40.2 - - + -
420A ILE* 3.4 33.3 - - + +
421A ARG* 3.7 11.9 - - + -
426A VAL* 3.6 23.8 - - + -
428A VAL* 3.6 27.3 - - + +
433A ILE* 3.9 14.1 - - + -
437A PRO* 2.7 34.2 + - + -
439A ILE* 3.2 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA 2.9 14.5 + - - +
87A TRP* 1.3 81.0 - - - +
89A ALA* 1.3 55.4 + - - +
91A MET* 3.2 5.9 + - - +
92A THR* 2.7 38.1 + - - +
149A ALA* 3.8 17.3 - - + -
152A PHE* 3.6 18.7 - - + -
153A LEU* 3.6 17.4 - - - +
162A LEU* 5.1 1.3 - - + -
438A TYR* 3.2 15.6 - - + -
439A ILE* 2.6 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE 3.0 18.5 + - - +
86A ARG 3.7 4.5 - - - +
88A ASN* 1.3 76.3 - - - +
90A ILE* 1.3 62.9 + - + +
92A THR* 3.6 4.6 + - - +
93A VAL* 3.3 28.2 + - - +
107A MET* 5.3 1.3 - - - -
110A PHE* 4.1 12.6 - - + -
111A GLN* 5.2 1.1 - - - +
145A PRO* 3.4 37.8 - - + +
146A GLY* 3.8 8.3 - - - +
149A ALA* 3.5 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 3.1 18.3 + - + +
87A TRP* 3.1 7.9 + - - +
89A ALA* 1.3 78.1 - - - +
91A MET* 1.3 73.7 + - + +
93A VAL* 3.4 1.0 + - - +
94A LEU* 2.9 55.0 + - + +
107A MET* 4.1 23.8 - - + -
111A GLN* 3.7 28.9 - - + +
396A MET* 4.8 7.2 - - + -
417A VAL* 5.6 3.8 - - + -
420A ILE* 3.5 36.8 - - + -
424A PHE* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TRP* 2.8 74.6 + - + +
88A ASN* 3.2 5.6 + - - +
90A ILE* 1.3 97.9 - - + +
92A THR* 1.3 57.2 + - - +
94A LEU* 3.8 2.9 - - + +
95A ARG* 2.8 37.0 + - - +
417A VAL* 4.3 11.9 - - + -
420A ILE* 5.6 0.2 - - + -
436A LEU* 3.5 42.8 - - + +
437A PRO 3.4 6.7 - - - +
438A TYR* 3.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN 2.7 29.7 + - - +
89A ALA* 3.9 8.8 + - - +
91A MET* 1.3 75.0 - - - +
93A VAL* 1.3 58.4 + - - +
95A ARG* 3.9 1.3 - - - +
96A ALA* 3.1 27.5 + - - +
145A PRO* 4.8 8.0 - - - +
148A TYR* 5.7 1.4 - - + -
149A ALA* 5.4 0.9 - - + -
162A LEU* 3.8 32.6 - - + +
165A PHE* 3.6 27.3 - - - +
438A TYR* 3.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ALA 3.3 17.5 + - - +
90A ILE 3.8 3.6 - - - +
91A MET 3.2 0.4 - - - -
92A THR* 1.3 76.9 + - - +
94A LEU* 1.3 59.5 + - + +
96A ALA* 3.4 2.6 + - - +
97A SER* 3.0 29.4 + - - -
104A GLY 4.6 3.6 - - - +
105A GLY* 3.8 24.0 - - - +
106A HIS 3.7 21.3 - - - +
107A MET* 3.9 22.0 - - + -
145A PRO* 3.8 18.4 - - + -
165A PHE* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ILE* 2.9 40.8 + - + +
91A MET* 3.8 6.1 - - + +
93A VAL* 1.3 77.0 - - + +
95A ARG* 1.3 59.0 + - - +
97A SER* 2.9 31.3 + - - +
98A LYS* 3.0 18.7 + - - +
107A MET* 3.2 31.9 - - + -
417A VAL* 4.9 16.8 - - + -
436A LEU* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET 2.8 28.1 + - - +
92A THR 3.9 3.6 - - - +
94A LEU* 1.3 68.7 - - - +
96A ALA* 1.3 65.8 + - - +
98A LYS* 3.3 30.0 + - - +
99A LYS* 3.6 13.5 + - - +
159A GLN* 3.4 17.8 + - - -
162A LEU 5.9 0.2 - - - +
163A ASP* 2.8 43.2 + - - +
435A LYS* 3.2 17.4 + - - +
436A LEU* 2.7 41.0 + - + +
437A PRO* 3.8 8.5 - - - +
438A TYR* 3.4 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR 3.1 19.5 + - - +
93A VAL* 3.6 4.9 - - - +
95A ARG* 1.3 77.8 - - - +
97A SER* 1.3 61.3 + - - +
99A LYS* 3.2 32.8 + - - +
100A ASP 4.2 1.2 + - - -
101A LEU 5.1 0.3 + - - -
103A LEU* 3.8 22.4 + - + +
104A GLY 4.8 2.9 - - - +
163A ASP 5.9 0.4 - - - -
165A PHE* 3.8 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A VAL* 3.0 16.6 + - - -
94A LEU* 2.9 28.0 + - - +
96A ALA* 1.3 74.2 - - - +
98A LYS* 1.3 65.6 + - - +
100A ASP* 3.1 15.4 + - - +
101A LEU 6.1 0.4 - - - +
103A LEU* 5.8 2.5 - - - +
104A GLY 5.6 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.0 12.6 + - + +
95A ARG* 3.3 21.6 - - - +
96A ALA 3.2 0.4 - - - -
97A SER* 1.3 77.3 + - - +
99A LYS* 1.3 62.3 + - + +
100A ASP* 3.1 6.2 + - - +
434A GLU 4.9 4.8 + - - -
435A LYS 4.7 6.1 + - - -
436A LEU* 3.5 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ARG* 3.7 10.5 - - - +
96A ALA* 3.3 22.2 - - - +
97A SER 3.1 0.8 - - - -
98A LYS* 1.3 78.4 - - + +
100A ASP* 1.3 66.9 + - - +
101A LEU* 3.3 24.1 + - + +
103A LEU* 3.9 8.3 - - + +
163A ASP 2.8 28.1 + - - -
164A ASN* 4.4 6.3 - - - +
165A PHE 4.9 2.6 + - - -
167A GLN* 2.7 36.8 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il