Contacts of the helix formed by residues 84 - 102 (chain B) in PDB entry 1LCP
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 GLU 84 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA* 3.9 18.5 - - + +
75B GLY 2.9 15.4 + - - +
77B ASP* 4.1 21.7 - - + +
82B TRP* 3.2 21.5 + - - +
83B HIS* 1.3 70.4 - - - +
85B GLY* 1.3 61.0 + - - +
87B GLU* 3.2 4.7 + - - +
88B ASN* 2.9 46.7 + - - +
501B MRD 5.0 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS 5.5 1.6 - - - -
72B LYS 5.9 1.3 - - - -
74B ALA* 3.3 27.7 + - - -
83B HIS* 3.3 9.0 - - - -
84B GLU* 1.3 76.6 - - - +
86B LYS* 1.3 63.6 + - - +
88B ASN* 3.2 8.2 + - - +
89B ILE* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B HIS* 3.1 42.9 - - + +
85B GLY* 1.3 74.8 - - - +
87B GLU* 1.3 57.5 + - - +
89B ILE* 3.3 4.9 + - - +
90B ARG* 3.0 55.2 + - - +
115B ASP* 2.9 35.8 + - - +
117B GLN* 5.9 2.6 - - - +
118B ALA* 4.0 10.9 - - + +
392B GLU* 3.2 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TRP* 3.8 44.3 - - + -
83B HIS 3.3 8.8 + - - +
84B GLU* 3.2 10.1 + - - +
86B LYS* 1.3 78.8 - - - +
88B ASN* 1.3 62.5 + - - +
90B ARG* 3.0 22.7 + - - +
91B ALA* 3.1 24.4 + - - +
394B GLY* 3.5 10.6 - - - -
460B VAL* 5.4 0.9 - - - +
461B PRO* 5.1 3.8 - - - +
462B TYR* 2.7 41.3 + - - -
501B MRD 3.9 23.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 4.4 7.7 - - + +
49B GLY 5.3 0.2 + - - -
68B GLY 4.8 0.9 - - - +
69B LEU* 3.3 29.1 - - - +
70B GLY* 4.1 7.3 - - - -
71B LYS 4.4 4.0 + - - +
74B ALA* 4.5 3.8 - - - +
84B GLU* 2.9 35.9 + - - +
85B GLY* 3.4 11.5 - - - +
87B GLU* 1.3 79.3 - - - +
89B ILE* 1.3 56.8 + - + +
91B ALA* 3.9 1.6 - - - +
92B ALA* 3.0 32.0 + - - +
501B MRD 3.7 40.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR* 6.4 1.1 - - + -
69B LEU* 4.4 15.7 - - + +
85B GLY* 3.0 19.7 + - - +
86B LYS* 3.6 6.1 - - - +
88B ASN* 1.3 74.4 - - + +
90B ARG* 1.3 65.6 + - - +
92B ALA 3.4 0.2 + - - -
93B VAL* 3.0 29.3 + - + +
113B CYS* 3.4 40.2 - - + +
114B GLY 5.0 0.2 - - - -
115B ASP* 3.6 24.2 - - + +
118B ALA* 3.9 4.3 - - + -
119B ALA* 3.6 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B HIS 4.9 0.8 + - - -
86B LYS* 3.0 45.8 + - - +
87B GLU* 3.0 28.4 + - - +
89B ILE* 1.3 74.3 - - - +
91B ALA* 1.3 63.4 + - - +
94B ALA* 3.1 25.3 + - - +
118B ALA* 3.6 18.9 - - + +
121B GLU* 2.9 30.8 + - + -
122B GLY* 3.4 19.2 - - - +
392B GLU* 3.0 23.8 + - - +
393B THR* 3.2 22.6 + - - +
394B GLY 4.1 0.4 - - - +
462B TYR* 3.5 41.1 - - + +
473B ARG* 3.7 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY* 4.9 4.0 - - - +
87B GLU 3.1 16.4 + - - +
88B ASN 3.9 3.1 - - - +
90B ARG* 1.3 77.4 - - - +
92B ALA* 1.3 62.4 + - - +
94B ALA* 3.4 3.5 + - - +
95B ALA* 3.0 24.0 + - - +
98B ARG* 5.2 0.7 + - - -
461B PRO* 3.7 30.6 - - + +
462B TYR* 3.9 10.9 - - + -
501B MRD 3.9 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY* 4.3 11.1 - - - -
67B VAL* 3.5 30.6 - - + +
68B GLY 3.3 26.0 - - - +
69B LEU* 3.9 10.1 - - + -
88B ASN 3.0 16.6 + - - +
89B ILE 4.0 0.4 - - - +
91B ALA* 1.3 77.2 - - - +
93B VAL* 1.3 57.0 + - - +
95B ALA* 3.3 4.5 + - - +
96B GLY 3.0 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 4.7 12.3 - - + +
67B VAL* 5.1 0.9 - - + -
89B ILE* 3.0 28.6 + - + +
90B ARG 4.3 1.3 - - - +
92B ALA* 1.3 76.6 - - + +
94B ALA* 1.3 63.1 + - - +
96B GLY* 3.2 2.1 + - - -
97B CYS* 2.9 26.2 + - - -
110B VAL* 3.6 25.8 - - + -
113B CYS* 4.1 25.4 - - - -
119B ALA* 3.4 27.6 - - - +
122B GLY* 4.6 0.7 - - - -
123B ALA* 3.7 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG 3.1 19.7 + - - +
91B ALA 3.6 4.0 - - - +
93B VAL* 1.3 77.7 - - - +
95B ALA* 1.3 63.2 + - - +
97B CYS* 3.3 4.0 + - - +
98B ARG* 3.0 34.7 + - - +
122B GLY 3.4 21.0 + - - +
126B GLY* 3.9 10.4 - - - -
462B TYR* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY 3.9 13.2 - - - +
51B THR* 3.6 23.9 + - + +
91B ALA 3.0 17.3 + - - +
92B ALA 3.6 3.1 - - - +
94B ALA* 1.3 76.5 - - - +
96B GLY* 1.3 62.1 + - - +
98B ARG* 3.3 28.2 + - - +
99B GLN* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.9 10.4 - - - +
51B THR* 4.0 0.8 - - - +
65B VAL* 4.0 12.9 - - - +
67B VAL* 3.8 22.2 - - - -
92B ALA 3.0 11.3 + - - -
93B VAL 3.2 3.8 + - - -
95B ALA* 1.3 77.6 - - - +
97B CYS* 1.3 59.8 + - - +
99B GLN* 3.2 5.9 + - - +
100B ILE* 3.2 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 4.5 5.4 - - - -
93B VAL* 2.9 26.4 + - - +
94B ALA* 3.8 5.6 - - - +
96B GLY* 1.3 72.6 - - - +
98B ARG* 1.3 66.6 + - - +
100B ILE* 3.2 9.2 + - - +
101B GLN* 3.0 23.6 + - - +
108B VAL* 4.4 13.2 - - + -
110B VAL* 4.1 15.7 - - - -
123B ALA* 3.8 28.3 - - - +
127B LEU* 3.9 28.3 - - + +
141B VAL* 5.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA 5.2 0.8 + - - -
94B ALA* 3.0 25.3 + - - +
95B ALA* 3.7 38.7 - - - +
96B GLY 3.3 0.2 - - - -
97B CYS* 1.3 77.2 - - - +
99B GLN* 1.3 57.6 + - - +
101B GLN* 3.3 8.6 + - - +
102B ASP* 3.0 28.1 + - - +
126B GLY 4.1 16.7 + - - +
127B LEU* 4.9 1.1 - - + -
461B PRO 3.3 25.1 + - - -
462B TYR* 4.7 2.0 - - - +
463B LEU 6.1 0.8 - - - -
464B ARG* 3.9 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 4.8 9.3 + - - +
53B THR* 3.0 31.6 + - - +
55B TYR* 4.4 4.5 + - - -
65B VAL* 3.8 16.6 - - + -
95B ALA 3.2 12.5 + - - +
96B GLY 3.5 9.4 - - - +
97B CYS 3.2 0.2 - - - -
98B ARG* 1.3 74.7 - - - +
100B ILE* 1.3 63.8 + - - +
102B ASP* 3.2 17.4 + - - +
103B LEU* 3.2 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLY* 3.9 19.5 - - - -
4B LEU 4.3 2.0 - - - +
5B VAL* 4.3 3.6 - - + -
63B SER* 4.1 11.0 - - - +
65B VAL* 3.6 24.2 - - + -
96B GLY 3.2 13.3 + - - +
97B CYS* 3.2 9.8 + - - +
99B GLN* 1.3 76.2 - - - +
101B GLN* 1.3 62.2 + - - +
103B LEU* 3.1 16.8 + - + +
105B ILE* 3.3 52.7 + - + +
107B SER 4.5 0.2 - - - +
108B VAL* 4.0 36.6 - - + -
141B VAL* 4.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B CYS 3.0 16.3 + - - +
98B ARG* 3.7 4.0 - - - +
100B ILE* 1.3 78.1 - - - +
102B ASP* 1.3 56.3 + - - +
104B GLU* 2.8 24.0 + - - +
105B ILE 4.7 1.6 - - - +
127B LEU* 3.7 20.3 - - + +
129B GLU* 4.6 1.6 - - - +
138B LYS* 3.8 25.7 - - + +
139B VAL* 2.9 32.1 + - + +
141B VAL* 3.8 19.9 + - + +
464B ARG* 2.7 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG 3.0 14.5 + - - +
99B GLN* 3.2 20.8 + - - +
101B GLN* 1.3 77.3 - - - +
103B LEU* 1.3 57.8 + - + +
104B GLU* 3.1 14.0 + - - +
138B LYS* 6.1 2.6 - - - -
----------------------------------------------------------
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