Contacts of the helix formed by residues 80 - 101 (chain D) in PDB entry 2Q7M
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 GLN 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D GLY 3.6 3.7 + - - +
8D ASN* 3.3 39.3 - - + +
9D VAL 3.2 10.5 - - - +
10D VAL 3.3 0.4 - - - +
11D LEU* 2.7 55.3 - - - +
12D LEU* 3.8 17.1 - - + +
75D GLY* 3.6 16.6 + - - +
79D SER* 1.3 71.7 - - - +
81D VAL* 1.3 62.5 + - + +
84D ALA* 3.1 23.9 + - - +
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Residues in contact with VAL 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.7 15.7 - - + -
79D SER* 4.1 9.9 - - - +
80D GLN* 1.3 80.1 - - + +
82D PRO* 1.3 75.0 - - + +
83D ALA 3.2 1.1 - - - -
84D ALA* 3.2 4.5 + - - +
85D PHE* 2.8 29.3 + - - +
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Residues in contact with PRO 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D CYS* 5.3 0.4 - - - -
79D SER* 2.8 38.8 - - - +
81D VAL* 1.3 100.9 - - + +
83D ALA* 1.3 60.6 + - - +
85D PHE* 3.0 6.7 + - + +
86D ALA* 2.8 37.1 + - - +
121D PHE* 4.5 9.0 - - + -
125D MET* 3.6 21.5 - - - -
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Residues in contact with ALA 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.0 2.9 - - + -
71D LEU* 3.6 17.8 - - - +
74D ALA* 3.0 15.0 - - + +
75D GLY* 3.4 15.3 - - - +
79D SER 3.3 9.9 - - - +
82D PRO* 1.3 81.1 - - - +
84D ALA* 1.3 58.7 + - - +
87D GLY* 3.0 23.9 + - - -
122D LEU* 3.8 6.3 - - - +
125D MET* 2.9 29.4 - - + +
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.4 41.1 - - + +
12D LEU* 4.1 7.2 - - + +
15D VAL* 3.6 11.3 - - + +
71D LEU* 4.6 4.7 - - - -
80D GLN 3.1 20.1 + - - +
81D VAL 3.2 3.5 + - - +
82D PRO 3.1 0.4 - - - -
83D ALA* 1.3 78.9 - - - +
85D PHE* 1.3 64.2 + - - +
87D GLY 3.6 0.3 + - - -
88D LEU* 3.1 19.2 + - - +
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Residues in contact with PHE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D VAL 2.8 20.1 + - - +
82D PRO* 3.7 6.7 - - + +
84D ALA* 1.3 70.0 - - - +
86D ALA* 1.3 66.9 + - + +
87D GLY 3.0 1.6 - - - -
88D LEU* 2.4 42.2 + - + +
89D MET* 2.9 51.8 + - + -
121D PHE* 6.3 0.7 - + - -
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Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D PRO 2.8 15.3 + - - +
85D PHE* 1.3 82.9 - - + +
87D GLY* 1.3 59.7 + - - +
89D MET* 3.1 7.6 + - - -
118D ILE* 2.8 36.2 - - + +
121D PHE* 3.7 20.6 - - + -
122D LEU* 3.2 33.4 - - + -
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Residues in contact with GLY 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 3.8 9.9 - - - +
67D PHE* 3.6 29.0 - - - -
71D LEU* 4.4 7.2 - - - -
83D ALA 3.0 17.7 + - - -
84D ALA 3.9 2.0 - - - -
85D PHE 3.0 0.2 - - - -
86D ALA* 1.3 77.5 - - - +
88D LEU* 1.3 59.1 + - - +
90D TYR* 3.5 13.0 - - - +
91D LEU* 3.5 7.6 + - - +
122D LEU* 4.0 5.3 - - - +
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Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 3.5 17.0 - - + -
18D ILE* 5.4 7.0 - - + -
84D ALA 3.1 13.0 + - - +
85D PHE* 2.4 34.7 + - + +
87D GLY* 1.3 70.9 - - - +
89D MET* 1.3 87.3 + - + -
91D LEU* 3.1 18.5 + - + +
92D PHE* 3.4 33.3 + - + -
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Residues in contact with MET 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D PHE* 2.9 52.1 + - + +
86D ALA* 4.0 2.9 - - - +
88D LEU* 1.3 94.2 - - - +
90D TYR* 1.3 52.4 + - - +
92D PHE* 2.5 44.1 + - + +
93D VAL* 2.8 20.2 + - + +
118D ILE* 3.2 17.7 - - + -
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Residues in contact with TYR 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ALA* 2.9 37.1 + - - +
67D PHE* 3.4 53.8 - + + +
86D ALA 3.1 0.8 + - - +
87D GLY 3.5 3.6 - - - +
89D MET* 1.3 75.1 - - - +
91D LEU* 1.3 59.5 + - + +
93D VAL* 3.4 8.3 - - + +
94D ARG* 2.9 53.3 + - + +
114D PHE* 3.9 18.9 - + - -
115D GLY* 4.7 3.8 - - - -
118D ILE* 2.8 42.2 - - + +
119D ILE* 4.1 23.5 - - + +
505E 2CS 5.0 2.2 - + - -
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 3.3 33.9 - - + +
18D ILE* 3.0 35.4 - - + -
19D SER* 3.4 27.8 - - - +
22D GLN* 3.2 34.2 + - + +
67D PHE* 4.0 15.9 - - + -
87D GLY 3.5 7.5 + - - +
88D LEU* 3.1 14.0 + - + +
89D MET 3.0 0.8 - - - -
90D TYR* 1.3 85.2 - - + +
92D PHE* 1.3 61.0 + - + +
94D ARG* 4.0 2.7 - - - +
95D GLN* 3.3 13.3 + - - +
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Residues in contact with PHE 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D LEU* 3.4 31.8 + - + -
89D MET* 2.5 40.4 + - + +
91D LEU* 1.3 75.2 - - + +
93D VAL* 1.3 57.4 + - + +
94D ARG 3.3 0.2 - - - -
95D GLN* 3.2 10.0 + - + +
96D LYS* 3.0 32.8 + - + +
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Residues in contact with VAL 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D MET* 2.8 20.9 - - + +
90D TYR* 3.4 20.2 - - + +
92D PHE* 1.3 71.9 - - + +
94D ARG* 1.3 54.5 + - - +
96D LYS* 3.0 6.5 + - + +
97D TYR* 2.6 41.2 + - + +
114D PHE* 4.4 7.6 - - + -
115D GLY* 4.7 20.0 - - - +
118D ILE* 4.4 9.0 - - + -
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Residues in contact with ARG 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D SER* 4.1 2.6 + - - -
22D GLN* 2.9 41.3 + - - +
23D ASN* 2.4 34.4 + - - -
26D PHE* 3.5 10.6 - - - -
60D CYS* 3.2 35.7 + - - +
64D TYR* 3.5 36.5 - - - +
90D TYR* 2.9 41.4 + - + +
91D LEU* 3.9 0.9 - - - +
93D VAL* 1.3 74.9 - - - +
95D GLN* 1.3 55.3 + - - +
97D TYR* 4.0 0.9 - - - +
98D PHE* 2.9 35.2 + - - +
114D PHE* 3.3 36.9 - - + -
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Residues in contact with GLN 95 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D GLN* 3.2 11.9 + - + +
25D PHE* 3.4 28.3 - - - -
26D PHE* 3.0 27.5 - - - -
91D LEU 3.3 11.6 + - - +
92D PHE* 3.2 14.3 + - + +
93D VAL 3.1 0.4 - - - -
94D ARG* 1.3 79.0 - - - +
96D LYS* 1.3 78.2 + - + +
98D PHE* 3.7 1.8 - - - -
99D VAL* 2.9 46.6 + - - +
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Residues in contact with LYS 96 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92D PHE* 3.0 19.0 + - + +
93D VAL* 3.4 7.9 - - + +
95D GLN* 1.3 97.6 - - + +
97D TYR* 1.3 59.7 + - - +
99D VAL* 3.9 23.8 - - + +
100D GLY* 3.5 15.2 + - - -
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Residues in contact with TYR 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ALA 4.1 6.7 - - - -
59D ASN* 2.8 36.6 + - + +
60D CYS* 3.7 22.2 - - - -
93D VAL* 2.6 21.2 + - + +
94D ARG 4.0 0.9 - - - +
96D LYS* 1.3 72.9 - - - +
98D PHE* 1.3 61.2 + - - +
99D VAL 2.9 8.6 + - - -
100D GLY* 3.5 0.9 + - - -
101D TYR* 3.1 35.8 + + - +
109D THR* 4.9 1.3 - - + +
110D PRO 3.7 8.3 - - - -
111D GLY* 3.1 28.6 - - - -
112D TYR* 2.9 9.9 + - - -
113D ILE* 4.6 10.8 - - + -
114D PHE* 3.8 38.8 - + + -
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Residues in contact with PHE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PHE* 4.2 18.6 - + - -
26D PHE* 3.0 68.6 - + + -
29D LYS* 4.3 13.0 - - + -
53D VAL* 4.3 11.4 - - + -
56D ALA* 3.6 24.6 - - + +
57D ASN* 3.5 28.5 - - + -
60D CYS* 4.0 6.1 - - - -
94D ARG 2.9 20.2 + - - +
95D GLN* 4.1 2.9 - - - +
97D TYR* 1.3 81.7 - - - +
99D VAL* 1.3 61.6 + - + +
101D TYR* 4.1 5.6 + - - +
102D LEU* 3.8 19.6 - - + +
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D PHE* 6.0 1.6 - - + -
95D GLN* 2.9 38.3 + - - +
96D LYS* 4.0 25.8 - - - +
97D TYR 2.9 0.4 - - - -
98D PHE* 1.3 78.7 - - + +
100D GLY* 1.3 69.0 + - - +
101D TYR 3.0 5.3 + - - -
102D LEU* 3.3 26.0 - - + +
103D GLY 4.0 2.3 + - - -
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Residues in contact with GLY 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D LYS 3.5 11.4 + - - -
97D TYR* 3.5 1.3 + - - -
99D VAL* 1.3 80.9 - - - +
101D TYR* 1.3 48.8 + - - +
102D LEU 2.8 17.1 + - - -
103D GLY* 3.7 9.2 + - - -
109D THR* 2.5 34.5 + - - +
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Residues in contact with TYR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ARG* 3.4 23.1 - - + +
55D THR* 3.2 29.4 - - + +
56D ALA* 2.9 33.8 - - + +
59D ASN* 3.4 20.6 + - - -
97D TYR* 3.1 27.9 + + - +
98D PHE 4.3 1.8 - - - -
99D VAL 3.0 1.0 - - - -
100D GLY* 1.3 73.7 - - - +
102D LEU* 1.3 70.3 + - - +
109D THR* 2.9 38.6 - - + +
110D PRO 4.2 2.9 - - - -
111D GLY* 4.0 10.8 - - - -
41E SER* 5.0 3.1 - - - -
42E PHE* 3.1 41.1 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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