Contacts of the helix formed by residues 64 - 84 (chain A) in PDB entry 4J6V
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 ALA 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA 3.5 20.9 - - - +
62A SER* 3.1 0.8 + - - -
63A SER* 1.3 71.7 - - - +
65A PHE* 1.3 64.8 + - - +
66A LEU 3.2 0.9 - - - -
67A PRO* 3.4 6.0 - - + +
68A TRP* 2.8 27.2 + - - +
250A TYR* 3.6 9.6 - - - +
259A GLY 3.8 16.4 - - - +
260A GLN* 2.8 21.5 + - - +
266A MET* 4.4 14.8 - - + -
273A PRO* 5.2 0.9 - - + -
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA 3.3 27.2 - - - +
60A HIS* 4.1 5.6 - + - -
62A SER* 3.1 16.7 + - - +
63A SER 3.1 1.2 - - - -
64A ALA* 1.3 77.4 - - - +
66A LEU* 1.3 87.8 + - + +
69A HIS* 2.6 49.8 + + + +
191A ARG* 4.2 6.3 - - - -
194A LEU 5.1 0.4 - - - -
195A GLU* 3.5 48.2 - - + +
204A HIS* 3.6 43.7 - + + -
231A HIS* 3.9 10.5 - + - -
234A VAL* 4.2 8.7 - - + -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER 4.0 1.4 + - - -
65A PHE* 1.3 90.0 - - + +
67A PRO* 1.3 73.3 - - + +
68A TRP 3.3 0.2 + - - -
69A HIS* 3.3 5.5 + - + +
70A ARG* 3.0 18.5 + - - +
177A TYR* 3.5 29.4 - - + +
190A PHE* 4.0 17.7 - - + -
191A ARG* 4.1 12.8 - - + +
194A LEU* 3.9 10.1 - - + -
234A VAL* 3.7 31.4 - - + +
235A ASP* 5.0 1.4 - - - +
238A TRP* 3.6 41.9 - - + -
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Residues in contact with PRO 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER 3.6 1.1 - - - +
64A ALA* 3.4 20.4 - - - +
66A LEU* 1.3 90.3 - - + +
68A TRP* 1.3 61.3 + - - +
70A ARG* 3.3 1.7 + - + +
71A GLU* 3.0 24.4 + - - +
177A TYR* 3.3 18.8 - - - +
238A TRP* 3.7 19.7 - - + -
250A TYR* 3.8 15.0 - - + -
266A MET* 3.7 14.7 - - - +
273A PRO* 3.8 14.4 - - + +
276A VAL* 3.7 21.4 - - + +
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Residues in contact with TRP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TRP 4.1 4.3 - - - -
42A HIS* 3.8 31.2 - + - -
45A ALA* 3.4 21.5 - - + +
58A ALA 3.4 20.2 - - - +
59A ALA* 3.5 16.4 - - + -
64A ALA 2.8 24.6 + - - +
65A PHE 4.0 2.5 - - - +
67A PRO* 1.3 73.7 - - - +
69A HIS* 1.3 70.8 + + - +
71A GLU* 3.3 3.1 + - - +
72A TYR* 3.0 64.4 + + + +
266A MET* 3.5 23.0 - - + -
267A TYR 2.7 27.7 + - - -
268A PRO* 3.9 7.6 - - + -
269A TRP* 3.5 22.7 - + - -
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Residues in contact with HIS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A HIS* 3.4 5.4 + - - -
59A ALA* 3.0 26.9 - - + -
60A HIS* 3.8 1.1 - - - -
65A PHE* 2.6 39.4 + + + +
66A LEU* 4.0 3.4 - - + +
68A TRP* 1.3 94.3 - + - +
70A ARG* 1.3 66.1 + - - +
72A TYR* 3.4 5.0 - + + +
73A LEU* 3.0 31.1 + - + +
227A PHE* 4.4 4.7 - + - -
231A HIS* 3.2 40.7 - + + +
234A VAL* 6.3 1.3 - - + -
235A ASP* 6.1 0.4 - - - -
401A CU 2.4 29.0 - - - -
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 5.4 0.5 + - - -
66A LEU 3.0 16.2 + - - +
67A PRO 3.3 5.1 + - - +
69A HIS* 1.3 76.6 - - - +
71A GLU* 1.3 57.1 + - - +
73A LEU* 3.5 4.3 + - - +
74A LEU* 3.0 27.7 + - - +
235A ASP* 2.6 41.6 + - - +
238A TRP* 3.2 32.4 - - + -
239A ALA* 3.8 11.5 - - - +
242A GLN* 3.1 20.2 + - - -
276A VAL* 3.0 21.1 + - + -
277A MET 2.6 30.5 + - - -
279A HIS* 3.9 13.5 - - - +
282A LEU* 3.9 15.5 - - + -
284A TYR* 3.3 20.7 + - - +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO 3.0 13.1 + - - +
68A TRP 3.6 7.6 - - - +
70A ARG* 1.3 74.2 - - - +
72A TYR* 1.3 65.8 + - - +
74A LEU* 3.2 16.7 + - - +
75A ARG* 2.7 53.8 + - - +
78A ARG* 5.2 3.8 + - - -
266A MET* 4.2 7.9 - - + -
269A TRP* 3.7 26.2 - - + -
271A THR* 3.0 25.2 + - + +
276A VAL* 3.3 23.4 - - + +
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Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 2.7 60.4 + + + +
41A TRP* 4.3 3.1 - - + -
42A HIS* 4.3 6.3 - + + -
68A TRP* 3.0 48.3 + + + +
69A HIS* 3.4 12.1 - + - +
71A GLU* 1.3 77.1 - - - +
73A LEU* 1.3 65.0 + - + +
75A ARG* 3.4 5.1 + - - +
76A PHE* 3.0 28.1 + - - +
222A PRO* 3.7 18.4 - - - +
227A PHE* 3.4 23.1 - + - -
228A PHE* 3.4 24.7 - + - -
269A TRP* 3.9 16.8 - + + -
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 4.0 15.6 + - - +
69A HIS* 3.0 21.4 + - + +
70A ARG* 3.9 4.0 - - - +
72A TYR* 1.3 79.5 - - + +
74A LEU* 1.3 60.7 + - - +
76A PHE* 3.3 4.1 + - - +
77A GLU* 2.8 31.4 + - - +
89A LEU* 3.7 26.0 - - + +
227A PHE* 5.5 0.2 - - + -
228A PHE* 3.8 31.6 - - + +
231A HIS* 3.4 45.1 - - + +
232A ALA* 3.5 10.1 - - - +
235A ASP* 4.2 8.5 - - + -
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 3.3 30.3 - - - +
8A ARG* 4.1 7.8 - - - +
70A ARG 3.0 18.5 + - - +
71A GLU* 3.2 21.3 + - - +
73A LEU* 1.3 77.0 - - - +
75A ARG* 1.3 61.7 + - - +
77A GLU* 3.4 1.9 + - - +
78A ARG* 3.0 61.3 + - - +
276A VAL* 5.0 0.2 - - + -
282A LEU* 3.7 42.0 - - + +
284A TYR* 4.2 11.0 - - + -
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.0 22.5 + - + +
41A TRP* 4.0 17.2 - - + -
71A GLU* 2.7 46.2 + - - +
72A TYR 3.7 4.0 - - - +
74A LEU* 1.3 76.3 - - - +
76A PHE* 1.3 62.7 + - - +
78A ARG* 3.3 18.5 + - - +
79A ASP* 3.0 18.9 + - - +
269A TRP* 3.3 49.5 - - - +
270A ASN 5.2 1.0 - - - +
271A THR* 3.4 13.5 + - - -
270B ASN* 3.7 24.5 - - - +
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Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 4.9 2.7 - + - -
26A VAL* 4.5 11.4 - - + -
29A LEU* 4.1 12.1 - - + +
35A TYR* 4.0 29.8 - + - -
38A TYR* 3.3 29.3 + + + -
72A TYR 3.0 17.0 + - - +
73A LEU* 3.5 6.7 - - - +
74A LEU 3.3 0.2 - - - -
75A ARG* 1.3 76.5 - - - +
77A GLU* 1.3 58.4 + - - +
79A ASP* 3.1 5.7 + - - +
80A LEU* 2.9 58.9 + - + +
89A LEU* 4.4 12.8 - - + -
228A PHE* 3.6 52.9 - + + -
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 2.9 33.7 + - - +
8A ARG* 2.9 39.8 + - - +
73A LEU 2.8 19.5 + - - +
74A LEU* 3.9 3.7 - - + +
76A PHE* 1.3 73.8 - - - +
78A ARG* 1.3 57.6 + - - +
80A LEU* 3.2 12.6 + - + +
81A GLN* 2.9 44.6 + - - +
87A VAL 4.9 0.2 - - - +
88A THR* 3.5 12.2 - - - -
89A LEU* 2.9 34.4 + - + +
284A TYR* 4.0 3.0 - - - +
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 5.1 11.1 - - - +
71A GLU* 5.2 4.4 + - - -
74A LEU* 3.0 54.8 + - + +
75A ARG* 3.5 20.9 - - - +
77A GLU* 1.3 75.3 - - - +
79A ASP* 1.3 64.5 + - - +
81A GLN* 3.5 9.4 + - - +
82A SER* 3.1 22.7 + - - -
282A LEU* 4.6 10.3 + - - +
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.8 20.9 - - + +
34A ILE* 3.5 22.1 - - + +
37A ARG* 5.5 1.9 + - - -
38A TYR* 2.6 33.5 + - + +
75A ARG 3.0 8.6 + - - +
76A PHE* 3.1 9.6 + - - +
78A ARG* 1.3 75.5 - - - +
80A LEU* 1.3 64.9 + - - +
82A SER* 2.8 24.5 + - - -
83A ILE* 3.5 11.4 + - - +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.9 19.3 - - + -
25A THR* 3.6 27.3 - - + +
26A VAL* 4.2 16.6 - - + +
29A LEU* 3.9 17.0 - - + -
76A PHE* 2.9 43.7 + - + +
77A GLU* 3.2 14.1 + - - +
79A ASP* 1.3 73.9 - - - +
81A GLN* 1.3 59.6 + - - +
83A ILE* 3.0 7.6 + - - +
84A ASN 2.9 27.0 + - - +
87A VAL* 4.1 22.0 - - + +
88A THR 4.6 0.7 - - - -
89A LEU* 4.5 11.9 - - - +
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Residues in contact with GLN 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 3.5 33.3 - - - +
77A GLU* 2.9 26.8 + - - +
78A ARG* 3.5 9.8 + - - +
80A LEU* 1.3 78.6 - - - +
82A SER* 1.3 60.4 + - - +
83A ILE 3.3 0.5 + - - -
84A ASN 3.6 5.2 - - - -
85A PRO* 3.1 50.2 + - + +
87A VAL 3.1 22.9 + - - +
88A THR* 4.1 6.3 - - - +
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Residues in contact with SER 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 5.5 0.2 - - - +
34A ILE* 6.0 2.1 - - - +
78A ARG 3.1 12.6 + - - -
79A ASP* 2.8 28.2 + - - -
81A GLN* 1.3 76.3 - - - +
83A ILE* 1.3 68.4 + - - +
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 3.9 17.3 - - + +
28A ILE* 3.8 33.4 - - + -
29A LEU* 3.6 27.1 - - + -
32A LYS* 3.6 35.2 - - + -
34A ILE* 5.6 1.8 - - + -
79A ASP 3.7 4.0 - - - +
80A LEU 3.0 6.4 + - - +
81A GLN 4.1 0.7 - - - -
82A SER* 1.3 88.8 - - - +
84A ASN* 1.3 60.7 + - + +
85A PRO* 4.2 4.6 - - - +
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Residues in contact with ASN 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASP* 4.4 19.0 + - - +
24A ARG* 4.5 8.9 - - - +
25A THR* 3.8 11.2 + - - +
80A LEU 2.9 13.6 + - - +
81A GLN* 3.4 6.2 - - - -
83A ILE* 1.3 81.4 - - + +
85A PRO* 1.3 64.9 - - - +
86A GLU* 3.0 29.3 + - - +
87A VAL* 3.0 36.6 + - + +
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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) + - + + + + + -
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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