Contacts of the helix formed by residues 80 - 100 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C GLY 3.4 3.8 + - - +
8C ASN* 2.8 41.8 - - + +
9C VAL 2.9 13.5 - - - +
10C VAL 3.2 0.8 - - - +
11C LEU* 2.7 55.0 - - - +
12C LEU* 3.8 17.8 - - + +
75C GLY* 3.5 17.3 + - - +
79C SER* 1.3 72.0 + - - +
81C VAL* 1.3 57.9 + - - +
84C ALA* 3.2 24.1 + - - +
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Residues in contact with VAL 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.6 13.2 - - + -
79C SER* 3.5 6.5 + - - +
80C GLN* 1.3 77.0 - - + +
82C PRO* 1.3 80.8 - - + +
83C ALA 3.2 0.9 - - - -
84C ALA* 3.1 5.5 + - - +
85C PHE* 2.9 22.2 + - + +
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Residues in contact with PRO 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C CYS* 5.1 0.4 - - - -
79C SER* 2.7 44.6 - - - +
81C VAL* 1.3 94.3 - - + +
83C ALA* 1.3 62.1 + - - +
85C PHE* 3.0 6.9 + - + +
86C ALA* 2.7 36.9 + - - +
121C PHE* 4.5 9.3 - - + -
125C MET* 3.6 23.1 - - - -
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 4.3 2.2 - - + -
71C LEU* 3.0 26.7 - - - +
74C ALA* 3.0 29.8 - - + +
75C GLY* 3.4 15.3 - - - +
79C SER 3.1 11.2 - - - +
82C PRO* 1.3 81.6 - - - +
84C ALA* 1.3 57.7 + - - +
87C GLY 3.1 15.1 + - - -
122C LEU* 3.8 4.5 - - - +
125C MET* 3.1 15.3 - - + -
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Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.4 36.8 - - + +
12C LEU* 4.1 8.5 - - + +
15C VAL* 3.5 13.9 - - + +
71C LEU* 4.4 4.3 - - - -
80C GLN 3.2 19.9 + - - +
81C VAL* 3.1 4.9 + - - +
83C ALA* 1.3 79.6 - - - +
85C PHE* 1.3 63.7 + - - +
88C LEU* 3.2 15.9 + - - +
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Residues in contact with PHE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C VAL* 2.9 16.9 + - + +
82C PRO* 3.7 6.5 - - + +
84C ALA* 1.3 75.7 - - - +
86C ALA* 1.3 64.8 + - + +
88C LEU* 2.5 42.4 + - + +
89C MET* 3.0 45.9 + - + -
121C PHE* 6.4 0.4 - + - -
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PRO 2.7 20.9 + - - +
85C PHE* 1.3 81.5 - - + +
87C GLY* 1.3 60.6 + - - +
89C MET* 3.1 10.9 + - - +
90C TYR 3.1 17.0 + - - -
118C ILE* 3.5 16.5 - - + +
121C PHE* 3.7 22.0 - - + -
122C LEU* 3.3 25.8 - - + -
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Residues in contact with GLY 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 3.6 9.3 - - - +
67C PHE* 3.8 16.1 - - - -
71C LEU* 3.8 17.3 - - - -
83C ALA 3.1 16.0 + - - -
84C ALA 4.0 1.1 - - - -
85C PHE 3.0 1.0 - - - -
86C ALA* 1.3 76.8 - - - +
88C LEU* 1.3 60.2 + - - +
90C TYR* 3.4 13.4 - - - +
91C LEU* 3.4 15.1 + - - +
122C LEU* 4.1 3.1 - - - +
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 3.6 14.1 - - + -
18C ILE* 5.3 8.7 - - + -
84C ALA 3.2 12.6 + - - +
85C PHE* 2.5 31.1 + - + +
87C GLY* 1.3 70.5 - - - +
89C MET* 1.3 87.1 + - - -
90C TYR 3.1 0.2 - - - -
91C LEU* 2.9 19.8 + - + +
92C PHE* 3.3 37.5 + - + -
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Residues in contact with MET 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C PHE* 3.2 48.5 - - + +
86C ALA* 3.1 10.1 + - - +
88C LEU* 1.3 96.3 - - - +
90C TYR* 1.3 54.9 + - - +
92C PHE* 2.5 45.1 + - + +
93C VAL* 2.8 15.3 + - + +
118C ILE* 3.6 15.3 - - + -
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Residues in contact with TYR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A 2CS 4.7 0.5 - - - -
63C ALA* 3.0 36.4 + - - +
67C PHE* 3.4 46.1 - + + +
86C ALA 3.1 7.6 + - - +
87C GLY 3.4 11.2 - - - +
89C MET* 1.3 81.3 - - - +
91C LEU* 1.3 65.8 + - + +
93C VAL* 3.8 3.0 - - + +
94C ARG* 3.0 49.0 + - + +
114C PHE* 3.0 24.5 + + - -
115C GLY* 4.8 1.8 - - - -
118C ILE* 3.3 28.0 - - + +
119C ILE* 3.5 29.2 - - + +
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 3.4 14.4 - - + +
18C ILE* 2.9 36.1 - - + -
19C SER* 3.3 31.6 - - - +
22C GLN* 3.6 23.2 + - - +
67C PHE* 4.0 7.4 - - + -
87C GLY 3.4 16.6 + - - +
88C LEU* 2.9 13.8 + - + +
90C TYR* 1.3 94.6 - - + +
92C PHE* 1.3 63.7 + - + +
94C ARG* 4.0 4.7 - - - +
95C GLN* 3.3 22.5 + - - +
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Residues in contact with PHE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LEU* 4.0 34.8 - - + -
89C MET* 2.5 40.3 + - + +
91C LEU* 1.3 79.4 - - + +
93C VAL* 1.3 62.6 + - + +
94C ARG 3.2 0.2 - - - -
95C GLN* 3.2 9.0 + - + +
96C LYS* 3.0 35.8 + - + +
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C MET* 2.8 16.4 + - + +
90C TYR* 3.8 4.9 - - + +
92C PHE* 1.3 75.2 - - + +
94C ARG* 1.3 54.1 + - - +
96C LYS* 3.2 5.1 + - + +
97C TYR* 2.7 39.5 + - + +
114C PHE* 4.5 13.0 - - + -
115C GLY* 4.0 26.0 - - - +
118C ILE* 3.4 25.8 - - + -
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Residues in contact with ARG 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C SER* 4.1 4.6 + - - -
22C GLN* 2.6 33.5 + - - +
23C ASN* 2.6 29.6 + - - -
26C PHE* 3.5 6.7 - - + -
60C CYS* 3.4 37.1 + - - -
64C TYR* 3.4 39.1 - - - +
90C TYR* 3.0 41.3 + - + +
91C LEU* 3.9 2.4 - - - +
92C PHE 3.2 0.2 - - - -
93C VAL* 1.3 77.7 - - - +
95C GLN* 1.3 57.5 + - - +
97C TYR* 4.2 2.3 - - - +
98C PHE* 2.9 34.0 + - - +
114C PHE* 2.9 37.5 - - + -
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Residues in contact with GLN 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLN* 2.9 27.1 + - - +
25C PHE* 4.1 24.7 - - - -
26C PHE* 3.1 10.8 - - - -
91C LEU 3.3 12.2 + - - +
92C PHE* 3.2 9.5 + - + +
93C VAL 3.1 0.4 - - - -
94C ARG* 1.3 79.6 - - - +
96C LYS* 1.3 83.4 + - - +
98C PHE* 4.1 11.1 - - - -
99C VAL* 2.9 37.4 + - - +
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Residues in contact with LYS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C PHE* 3.0 28.5 + - + +
93C VAL* 4.0 5.6 - - + +
95C GLN* 1.3 103.4 - - - +
97C TYR* 1.3 58.9 + - - +
99C VAL* 3.9 15.8 - - + +
100C GLY* 3.4 15.4 + - - -
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Residues in contact with TYR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA* 4.0 8.1 - - - -
59C ASN* 2.7 38.3 + - + +
60C CYS* 3.6 29.6 - - - -
93C VAL* 2.7 22.8 + - + +
94C ARG 4.4 1.3 - - - -
96C LYS* 1.3 70.6 - - - +
98C PHE* 1.3 68.3 + - - +
99C VAL 3.0 5.4 + - - -
100C GLY* 3.4 1.1 + - - -
101C TYR* 3.1 42.2 + + - +
109C THR* 4.9 9.6 - - + +
111C GLY* 2.8 28.6 + - - -
112C TYR* 4.1 1.0 - - - -
113C ILE 4.7 0.9 - - - -
114C PHE* 3.7 40.8 - + + -
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Residues in contact with PHE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PHE* 4.2 16.8 - + - -
26C PHE* 3.3 69.1 - + + -
29C LYS* 4.1 15.0 - - + -
53C VAL* 4.4 11.9 - - + -
56C ALA* 3.5 23.1 - - + -
57C ASN* 3.8 23.8 - - + -
60C CYS* 4.2 2.7 - - - -
94C ARG 2.9 20.7 + - - +
95C GLN* 4.0 9.9 - - - +
97C TYR* 1.3 82.5 - - - +
99C VAL* 1.3 61.3 + - + +
101C TYR* 4.1 5.1 + - - +
102C LEU* 4.1 14.2 - - + +
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PHE* 6.1 3.4 - - + -
95C GLN* 2.9 27.8 + - - +
96C LYS* 4.0 19.1 - - + +
97C TYR 3.0 0.2 - - - -
98C PHE* 1.3 79.9 - - + +
100C GLY* 1.3 67.8 + - - +
101C TYR 3.0 6.0 + - - -
102C LEU* 4.3 4.1 - - - +
103C GLY* 4.0 14.6 + - - -
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Residues in contact with GLY 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LYS 3.4 8.1 + - - -
97C TYR 3.4 3.5 + - - -
99C VAL* 1.3 84.7 - - - +
101C TYR* 1.3 56.8 + - - +
102C LEU 3.0 7.8 + - - -
103C GLY 4.5 0.9 - - - -
104C GLU* 4.0 17.7 + - - +
105C ARG 4.5 1.4 + - - -
109C THR* 2.8 30.8 + - - +
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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