Contacts of the helix formed by residues 66 - 86 (chain A) in PDB entry 4I6J
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 GLY 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER 4.3 1.4 + - - -
65A VAL* 1.3 77.1 - - - +
67A ILE* 1.3 70.6 + - - -
68A ASN 3.2 3.3 + - - -
69A ARG* 3.4 4.0 + - - +
70A TRP* 3.2 20.1 + - - -
218A PHE* 4.2 3.6 - - - -
401A GLU* 3.1 21.7 + - - +
402A LEU* 5.1 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY* 1.3 73.9 - - - -
68A ASN* 1.3 85.2 + - + +
70A TRP* 3.0 3.3 + - - -
71A ARG* 2.6 38.2 + - + +
213A LEU* 4.0 19.5 - - + -
218A PHE* 3.5 43.7 - - + -
219A PRO* 4.8 9.4 - - + +
223A LEU* 5.5 10.8 - - + -
366A ARG* 4.8 7.2 - - + +
402A LEU* 6.1 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY 3.2 1.2 - - - -
67A ILE* 1.3 91.5 - - + +
69A ARG* 1.3 56.9 + - - +
71A ARG* 3.8 11.7 + - - +
72A PHE* 2.8 23.6 + - - +
223A LEU* 5.7 5.4 - - - +
365A LEU 4.5 0.2 + - - -
366A ARG 3.2 16.8 + - - -
367A GLN 3.1 29.7 + - - +
368A GLU 3.6 16.9 - - - +
369A GLY* 3.6 6.6 - - - +
401A GLU 6.1 0.4 - - - +
402A LEU* 4.8 7.4 + - - +
404A LEU* 3.3 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER 4.6 1.0 + - - -
65A VAL* 3.0 40.5 - - + +
66A GLY* 3.4 4.5 + - - +
67A ILE 3.2 0.2 - - - -
68A ASN* 1.3 74.0 - - - +
70A TRP* 1.3 67.9 + - - +
72A PHE* 3.0 3.5 + - - +
73A LEU* 2.9 24.4 + - - +
274A ARG* 3.0 24.0 - - - +
275A PHE* 4.3 13.3 - - + -
400A ASP* 2.7 40.1 + - - -
401A GLU 3.7 14.5 + - - -
402A LEU 4.7 2.2 + - - +
403A LEU 3.4 18.2 + - - +
404A LEU* 3.7 22.9 - - + +
406A ALA 2.8 29.7 + - - -
407A ASP* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.5 16.2 - - + -
56A ASP 4.9 3.8 - - - -
59A PHE 4.7 2.2 - - - -
60A ALA* 3.5 45.0 + - + -
65A VAL* 3.1 48.2 + - + +
66A GLY 3.2 20.9 + - - -
67A ILE 3.0 5.7 + - - +
69A ARG* 1.3 78.3 - - - +
71A ARG* 1.3 64.1 + - - +
73A LEU* 3.1 30.0 + - + +
74A LEU* 3.0 34.0 + - + +
213A LEU* 4.1 5.8 - - + -
216A LEU* 4.1 19.1 - - + -
218A PHE* 3.4 26.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 2.6 22.9 + - + +
68A ASN* 3.9 10.8 + - - +
70A TRP* 1.3 73.8 - - - +
72A PHE* 1.3 64.4 + - - +
74A LEU* 3.5 4.3 + - - +
75A GLN* 3.0 54.1 + - + +
213A LEU* 3.9 27.7 - - + +
223A LEU* 3.4 31.6 - - - +
224A GLY 2.6 29.5 + - - -
225A PRO* 3.4 3.2 + - - +
226A ALA* 3.0 35.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN 2.8 19.5 + - - +
69A ARG* 3.0 4.5 + - - +
71A ARG* 1.3 78.7 - - - +
73A LEU* 1.3 61.0 + - - +
75A GLN* 3.3 4.9 + - - +
76A SER* 2.9 42.9 + - - -
228A TRP* 3.3 28.9 - - + -
230A GLY* 3.6 15.1 - - - -
271A PRO* 4.0 20.2 - - + -
272A TYR* 3.4 36.8 - + - -
275A PHE* 3.5 39.7 - + + -
277A CYS* 4.1 2.9 - - - -
404A LEU* 3.6 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG 5.3 1.1 - - - +
31A LEU* 3.6 28.5 - - + -
53A TYR* 3.3 37.5 - - + +
55A LEU* 5.4 2.2 - - + -
69A ARG 2.9 12.7 + - - +
70A TRP* 3.1 35.4 + - + +
72A PHE* 1.3 74.9 - - - +
74A LEU* 1.3 61.5 + - + +
76A SER* 3.0 7.3 + - - -
77A LEU* 2.9 41.1 + - + +
275A PHE* 4.1 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.6 4.9 - - + -
70A TRP* 3.0 24.4 + - + +
71A ARG* 4.1 4.5 - - - +
73A LEU* 1.3 76.8 - - + +
75A GLN* 1.3 59.8 + - + +
77A LEU* 3.3 14.9 + - + +
78A GLU* 2.7 35.7 + - + +
210A VAL* 3.8 6.7 - - + +
211A PRO* 3.7 41.7 - - + +
212A SER* 4.1 2.9 - - - -
213A LEU* 3.9 40.4 - - + +
216A LEU* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 3.0 55.3 + - + +
72A PHE* 3.7 4.6 - - - +
73A LEU 3.1 0.8 - - - -
74A LEU* 1.3 75.8 - - + +
76A SER* 1.3 61.5 + - - +
78A GLU* 3.7 7.4 - - - +
79A ASP* 2.9 30.5 + - - +
226A ALA* 4.1 6.5 - - - +
228A TRP 4.4 0.5 - - - +
229A GLN* 3.1 33.4 + - - +
230A GLY* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.9 24.8 - - - +
72A PHE* 2.9 23.5 + - - -
73A LEU* 3.0 8.3 + - - -
75A GLN* 1.3 77.2 - - - +
77A LEU* 1.3 58.5 + - - +
79A ASP* 3.2 4.3 + - - +
80A LEU* 2.8 32.5 + - - +
230A GLY 3.9 0.4 - - - -
231A GLY* 3.3 28.8 + - - -
232A GLU 5.2 0.3 + - - -
275A PHE* 4.8 0.3 - - - -
277A CYS* 3.5 13.4 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
27A PHE* 5.6 0.9 - - + -
31A LEU* 4.6 12.1 - - + -
53A TYR* 4.0 45.8 - - + -
55A LEU* 4.6 7.2 - - + -
73A LEU* 2.9 33.4 + - + +
74A LEU* 3.5 15.7 - - + +
76A SER* 1.3 75.2 - - - +
78A GLU* 1.3 55.3 + - - +
80A LEU* 3.1 9.4 + - + +
81A ASP* 2.7 35.2 + - - +
91A LEU* 3.4 20.6 - - + +
93A VAL* 4.7 7.6 - - + -
210A VAL* 3.9 19.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
74A LEU* 2.7 30.1 + - + +
75A GLN* 3.7 8.5 - - + +
77A LEU* 1.3 72.0 - - - +
79A ASP* 1.3 56.9 + - - +
81A ASP* 3.2 14.1 + - - +
82A THR* 2.9 34.5 + - - +
85A ARG* 5.5 1.6 + - - -
210A VAL* 3.7 35.0 - - + +
211A PRO 4.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLN 2.9 17.9 + - - +
76A SER 3.5 4.7 - - - +
78A GLU* 1.3 73.6 - - - +
80A LEU* 1.3 60.8 + - - +
82A THR* 3.5 9.1 - - - +
83A SER* 2.8 34.3 + - - -
230A GLY 4.5 3.0 - - - +
231A GLY* 3.7 9.5 - - - -
232A GLU* 3.4 8.3 + - - +
233A THR* 2.6 50.7 + - - -
234A GLU 4.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 4.0 24.5 - - + -
31A LEU* 3.6 45.3 - - + +
32A ARG* 3.9 14.1 - - - +
33A LEU* 4.0 33.4 - - + -
76A SER 2.8 13.8 + - - +
77A LEU* 3.3 14.6 - - + +
79A ASP* 1.3 77.5 - - - +
81A ASP* 1.3 56.0 + - - +
83A SER* 3.0 5.4 + - - -
84A LEU* 2.9 38.1 + - + +
91A LEU* 4.6 8.5 - - + -
232A GLU* 4.2 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU 2.7 16.2 + - - +
78A GLU* 3.2 23.9 - - - +
80A LEU* 1.3 74.8 - - - +
82A THR* 1.3 56.6 + - - +
84A LEU* 3.2 4.3 + - - +
85A ARG* 3.1 40.7 + - - +
90A ARG* 3.1 34.4 + - - +
91A LEU* 3.2 37.4 + - + +
210A VAL* 4.2 10.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 2.9 20.4 + - - +
79A ASP* 3.5 11.4 - - - +
81A ASP* 1.3 73.9 - - - +
83A SER* 1.3 67.0 + - - +
85A ARG* 3.2 27.5 + - - +
86A LYS* 3.3 12.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
33A LEU* 3.8 22.6 - - - +
79A ASP* 2.8 32.7 + - - -
80A LEU* 3.4 9.9 - - - -
82A THR* 1.3 73.7 - - - +
84A LEU* 1.3 62.8 + - - +
86A LYS* 3.5 18.7 - - - +
87A LEU* 3.6 13.7 + - - +
232A GLU* 4.4 9.6 + - - -
233A THR* 4.4 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 5.1 3.4 - - + -
33A LEU* 3.9 31.4 - - + -
39A LEU* 6.2 0.2 - - + -
51A CYS* 3.9 27.6 - - + -
80A LEU* 2.9 18.5 + - + +
81A ASP 3.5 5.6 - - - +
83A SER* 1.3 74.6 - - - +
85A ARG* 1.3 62.0 + - - +
86A LYS 3.2 0.2 - - - -
87A LEU* 2.9 24.1 + - + +
89A SER* 2.9 28.5 + - - +
90A ARG* 3.2 37.9 - - - +
91A LEU* 3.7 15.0 - - + +
193A MET* 5.4 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 5.5 1.6 + - - -
81A ASP* 3.1 38.5 + - - +
82A THR* 3.5 18.3 + - - +
84A LEU* 1.3 73.5 - - - +
86A LYS* 1.3 54.6 + - - +
87A LEU 2.8 4.9 - - - -
88A ASN* 2.7 26.8 + - - +
89A SER 3.6 6.5 - - - -
90A ARG* 3.4 45.7 - - + +
206A ASP* 5.5 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A THR 3.3 8.0 + - - +
83A SER* 3.5 14.6 - - - +
85A ARG* 1.3 77.2 - - - +
87A LEU* 1.3 71.7 + - + +
88A ASN* 3.5 6.8 - - - +
190A SER* 5.4 0.5 - - - -
197A ARG* 4.9 0.9 + - - -
----------------------------------------------------------
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