Contacts of the helix formed by residues 79 - 100 (chain A) 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 SER 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A GLY 3.8 0.4 - - - -
76A LEU 4.9 0.2 + - - -
78A CYS* 1.3 83.9 - - - +
80A GLN* 1.3 59.6 + - - +
81A VAL* 3.1 15.1 - - - +
82A PRO* 2.8 48.9 - - - +
83A ALA* 3.3 8.0 - - - +
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Residues in contact with GLN 80 (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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7A GLY 3.5 3.6 - - - +
8A ASN* 3.0 37.7 - - + +
9A VAL 2.6 30.7 - - - +
11A LEU* 2.8 59.2 - - + +
12A LEU* 3.6 19.6 - - + +
75A GLY 3.5 15.5 + - - +
79A SER* 1.3 71.3 + - - +
81A VAL* 1.3 59.3 + - + +
84A ALA* 3.1 18.9 + - - +
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.9 13.5 - - + -
79A SER* 3.3 16.4 - - - +
80A GLN* 1.3 76.8 - - + +
82A PRO* 1.3 64.1 - - + +
83A ALA 3.2 1.1 - - - -
84A ALA* 3.1 4.3 + - - +
85A PHE* 2.8 29.2 + - - +
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Residues in contact with PRO 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A CYS* 5.1 0.2 - - - -
79A SER* 2.8 42.4 - - - +
81A VAL* 1.3 95.4 - - + +
83A ALA* 1.3 60.0 + - - +
85A PHE* 3.0 6.1 + - + +
86A ALA* 2.7 37.1 + - - +
121A PHE* 4.3 9.4 - - + -
125A MET* 3.4 23.6 - - + -
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Residues in contact with ALA 83 (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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12A LEU* 4.1 2.9 - - + -
71A LEU* 3.5 19.0 - - - +
74A ALA* 2.9 32.1 - - + +
75A GLY* 3.4 15.3 - - - -
79A SER 3.3 9.6 - - - +
80A GLN 4.5 0.2 - - - -
82A PRO* 1.3 81.5 - - - +
84A ALA* 1.3 56.7 + - - +
86A ALA 3.7 0.2 + - - -
87A GLY 3.0 23.2 + - - -
122A LEU* 3.7 4.2 - - - +
125A MET* 3.0 12.8 - - + -
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Residues in contact with ALA 84 (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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11A LEU* 3.3 32.1 - - + +
12A LEU* 4.0 9.2 - - + +
15A VAL* 3.5 13.1 - - + +
71A LEU* 4.8 4.0 - - - -
80A GLN 3.1 20.5 + - - +
81A VAL* 3.1 5.7 + - + +
83A ALA* 1.3 77.5 - - - +
85A PHE* 1.3 63.5 + - - +
87A GLY 3.7 0.2 + - - -
88A LEU* 3.2 18.7 + - - +
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Residues in contact with PHE 85 (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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81A VAL 2.8 13.4 + - - +
82A PRO* 3.5 9.6 - - + +
84A ALA* 1.3 74.0 - - - +
86A ALA* 1.3 61.2 + - - +
87A GLY 3.0 1.8 - - - -
88A LEU* 2.4 43.3 + - + +
89A MET* 3.0 45.7 + - + -
121A PHE* 6.5 0.4 - + - -
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Residues in contact with ALA 86 (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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82A PRO 2.7 11.7 + - - +
85A PHE* 1.3 77.8 - - - +
87A GLY* 1.3 58.2 + - - +
89A MET* 3.2 3.8 + - - +
90A TYR 3.1 4.2 + - - -
118A ILE* 3.0 36.4 - - + +
121A PHE* 3.2 31.9 - - + -
122A LEU* 2.9 30.7 - - + -
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Residues in contact with GLY 87 (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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15A VAL* 3.7 7.9 - - - +
67A PHE* 3.6 19.8 - - - -
71A LEU* 3.6 27.6 - - - -
83A ALA 3.0 10.0 + - - -
84A ALA 4.0 0.4 - - - -
85A PHE 3.0 0.6 - - - -
86A ALA* 1.3 77.1 - - - +
88A LEU* 1.3 60.8 + - - +
90A TYR* 3.5 4.8 - - - +
91A LEU* 3.5 18.5 + - - +
122A LEU* 4.1 2.2 - - - +
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Residues in contact with LEU 88 (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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15A VAL* 3.6 15.3 - - + -
18A ILE* 5.1 7.6 - - + -
84A ALA 3.2 12.6 + - - +
85A PHE* 2.4 38.5 + - + +
87A GLY* 1.3 68.8 - - - -
89A MET* 1.3 74.8 + - + -
91A LEU* 3.0 23.4 + - + +
92A PHE* 3.2 49.3 + - + -
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Residues in contact with MET 89 (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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85A PHE* 3.0 48.9 + - + +
86A ALA* 3.6 3.6 - - - +
88A LEU* 1.3 91.7 - - + +
90A TYR* 1.3 57.6 + - - +
92A PHE* 2.6 45.3 + - + +
93A VAL* 2.9 16.8 + - + +
118A ILE* 3.2 21.8 - - + -
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Residues in contact with TYR 90 (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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63A ALA* 3.0 34.5 + - - +
67A PHE* 3.4 40.7 - + + +
86A ALA 3.1 11.7 + - - +
87A GLY 3.5 11.7 - - - +
89A MET* 1.3 76.5 - - - +
91A LEU* 1.3 56.6 + - + +
93A VAL* 3.6 6.0 + - - +
94A ARG* 3.0 57.2 + - + +
114A PHE* 3.6 18.0 - + - -
115A GLY* 4.8 4.3 - - - -
118A ILE* 3.3 21.0 - - + +
119A ILE* 3.6 34.9 - - + +
503A 2CS 4.4 4.3 - - - -
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Residues in contact with LEU 91 (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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15A VAL* 3.4 24.9 - - + +
18A ILE* 2.9 36.1 - - + -
19A SER* 3.3 34.5 - - - +
22A GLN* 3.6 23.1 + - + +
67A PHE* 3.8 17.5 - - + -
87A GLY 3.5 8.5 + - - +
88A LEU* 3.0 16.2 + - + +
89A MET 3.0 0.4 - - - -
90A TYR* 1.3 82.0 - - + +
92A PHE* 1.3 63.2 + - + +
94A ARG* 4.0 4.7 - - - +
95A GLN* 3.4 19.2 + - - +
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Residues in contact with PHE 92 (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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18A ILE* 6.5 0.4 - - + -
88A LEU* 3.2 42.2 - - + -
89A MET* 2.6 42.0 + - + +
91A LEU* 1.3 78.3 - - + +
93A VAL* 1.3 58.2 + - + +
94A ARG 3.2 0.9 - - - -
95A GLN* 3.2 5.8 + - + +
96A LYS* 2.9 39.1 + - + +
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Residues in contact with VAL 93 (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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89A MET* 2.9 20.8 + - + +
90A TYR* 3.9 8.5 - - + +
92A PHE* 1.3 74.4 - - + +
94A ARG* 1.3 53.5 + - - +
96A LYS* 3.0 7.6 + - + +
97A TYR* 2.6 39.4 + - + +
114A PHE* 3.5 22.7 - - + -
115A GLY* 4.0 21.5 - - - +
118A ILE* 4.7 9.4 - - + -
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Residues in contact with ARG 94 (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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19A SER* 4.4 4.4 + - - -
22A GLN* 2.4 33.8 + - - +
23A ASN* 2.7 31.8 + - - +
26A PHE* 3.8 7.9 - - - -
60A CYS* 3.4 40.2 + - - -
63A ALA* 4.1 0.2 - - - +
64A TYR* 3.3 36.4 - - - +
67A PHE* 4.8 1.1 - - - -
90A TYR* 3.0 53.4 + - + +
91A LEU* 3.8 4.7 - - - +
93A VAL* 1.3 77.7 - - - +
95A GLN* 1.3 57.6 + - - +
97A TYR* 4.1 0.2 - - - +
98A PHE* 2.9 34.7 + - - +
114A PHE* 3.1 31.8 - - + -
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Residues in contact with GLN 95 (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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22A GLN* 3.5 8.2 + - - +
25A PHE* 4.1 17.5 - - - -
26A PHE* 2.9 28.9 - - - -
91A LEU 3.4 12.7 + - - +
92A PHE* 3.2 12.4 + - + +
93A VAL 3.1 0.4 - - - -
94A ARG* 1.3 80.5 - - - +
96A LYS* 1.3 75.2 + - + +
98A PHE* 4.0 10.1 - - - -
99A VAL* 2.9 50.9 + - - +
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Residues in contact with LYS 96 (chain A).
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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92A PHE* 2.9 21.8 + - + +
93A VAL* 3.7 7.2 - - + +
95A GLN* 1.3 99.3 + - + +
97A TYR* 1.3 59.7 + - - +
99A VAL* 3.5 18.5 - - + +
100A GLY* 3.4 15.8 + - - -
109A THR* 5.3 2.3 + - - +
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Residues in contact with TYR 97 (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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56A ALA 5.2 0.4 - - - -
59A ASN* 3.2 22.6 + - + -
60A CYS* 4.4 8.7 - - - -
93A VAL* 2.6 20.9 + - + +
94A ARG 4.1 0.9 - - - +
96A LYS* 1.3 72.5 - - - +
98A PHE* 1.3 58.3 + - - +
99A VAL 2.9 8.6 + - - -
100A GLY 3.5 0.3 + - - -
101A TYR* 3.1 46.4 + + - +
109A THR* 3.6 13.4 + - - -
110A PRO 4.1 5.2 - - - -
111A GLY 3.2 15.8 + - - -
112A TYR* 2.8 36.5 - - - +
114A PHE* 3.2 53.2 - + + -
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Residues in contact with PHE 98 (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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25A PHE* 3.6 19.3 - + - -
26A PHE* 3.0 72.5 - + + -
29A LYS* 4.0 20.6 - - + -
53A VAL* 4.9 11.0 - - + -
56A ALA* 3.9 29.4 - - + +
57A ASN* 4.3 6.3 - - + -
60A CYS* 4.0 9.2 - - - -
94A ARG 2.9 17.3 + - - +
95A GLN* 4.0 9.6 - - - -
97A TYR* 1.3 77.5 - - - +
99A VAL* 1.3 61.4 + - + +
101A TYR* 4.2 8.2 + - - +
102A LEU* 4.5 7.3 - - - +
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Residues in contact with VAL 99 (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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95A GLN* 2.9 31.2 + - - +
96A LYS* 3.5 26.5 - - + +
97A TYR 2.9 0.8 - - - -
98A PHE* 1.3 78.6 - - + +
100A GLY* 1.3 70.9 + - - +
101A TYR 3.1 1.1 - - - -
102A LEU* 3.1 29.3 + - + +
103A GLY 3.8 3.3 + - - -
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Residues in contact with GLY 100 (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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96A LYS 3.4 9.2 + - - -
97A TYR 3.5 0.6 + - - -
99A VAL* 1.3 81.5 - - - +
101A TYR* 1.3 55.9 + - - +
102A LEU 2.9 14.5 + - - -
103A GLY* 4.3 2.5 + - - -
107A GLN 4.7 0.3 - - - +
108A SER* 3.3 8.5 + - - -
109A THR* 3.1 31.3 + - - +
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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