Contacts of the strand formed by residues 74 - 82 (chain C) in PDB entry 6QPA
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 MET 74 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C LYS* 3.4 3.6 - - - -
15C ILE* 2.9 51.0 + - + +
16C ALA 4.7 0.7 - - - +
17C ASN* 3.7 28.7 - - + +
22C TYR* 3.4 30.7 - - - +
49C LEU* 3.9 25.4 - - + -
50C GLN 3.3 23.1 - - - +
68C ARG* 5.0 10.3 - - + +
71C LEU* 4.0 23.6 - - + +
72C ASN* 4.1 0.4 - - - +
73C PRO* 1.3 75.2 - - - +
75C GLY* 1.3 62.8 + - - +
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Residues in contact with GLY 75 (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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13C ALA 3.6 7.2 - - - -
14C LYS* 4.4 9.9 - - - +
49C LEU* 3.8 5.0 - - - +
50C GLN* 2.9 52.8 + - - +
73C PRO 4.3 0.2 + - - -
74C MET* 1.3 74.8 - - - +
76C MET* 1.3 60.7 + - - +
77C PHE* 4.2 3.6 - - - -
297C MET* 4.5 9.2 - - - -
299C PHE* 4.4 3.1 - - - -
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Residues in contact with MET 76 (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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11C ASN 3.4 3.8 - - - +
13C ALA* 2.8 43.3 + - + +
15C ILE* 4.1 23.8 - - + -
25C MET* 4.1 22.4 - - + +
47C GLN* 4.4 22.4 - - + +
48C LEU 3.5 7.4 - - - +
49C LEU* 3.8 23.1 - - + -
75C GLY* 1.3 72.7 - - - -
77C PHE* 1.3 65.9 + - - +
78C GLN* 4.5 9.9 - - + +
109C MET* 4.4 18.6 - - + -
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Residues in contact with PHE 77 (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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10C ILE* 3.8 21.3 - - + -
11C ASN 3.4 2.9 - - - -
12C MET* 3.8 42.2 - - + -
13C ALA 4.7 3.6 - - - -
14C LYS* 6.4 0.9 - - + -
46C GLU 3.6 1.6 - - - +
47C GLN* 3.9 0.5 - - - -
48C LEU* 2.8 49.7 + - + +
75C GLY* 4.2 1.1 - - - -
76C MET* 1.3 87.6 - - - +
78C GLN* 1.3 59.5 + - - +
79C TYR* 4.0 6.1 - + + -
162C ILE* 3.7 27.4 - - + -
254C LEU* 4.8 7.0 - - + -
297C MET* 4.3 19.3 - - + -
299C PHE* 3.9 24.7 - + + -
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Residues in contact with GLN 78 (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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9C ALA 3.2 4.5 - - - +
10C ILE* 3.4 0.2 - - - -
11C ASN* 2.9 49.4 + - + +
32C VAL* 6.6 0.2 - - + -
33C CSS 3.5 19.8 - - - -
45C PHE* 3.2 35.8 - - - +
46C GLU 3.4 7.0 + - - -
47C GLN* 3.1 36.9 + - - +
76C MET* 4.1 8.8 + - - +
77C PHE* 1.3 72.1 - - - +
79C TYR* 1.3 68.9 + - - +
80C THR* 3.6 13.1 + - + +
116C GLU* 5.1 0.2 - - - +
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Residues in contact with TYR 79 (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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8C ILE* 4.0 20.6 - - + -
9C ALA 3.3 5.6 - - - -
10C ILE* 3.6 27.6 - - + -
45C PHE* 3.1 10.0 - - - +
46C GLU* 2.8 52.6 + - + +
48C LEU* 3.6 23.1 - - + -
77C PHE* 4.4 3.4 - - + -
78C GLN* 1.3 73.7 - - - +
80C THR* 1.3 60.9 + - - +
81C VAL* 4.3 5.2 - - + -
162C ILE* 3.3 22.1 - - + +
197C MET* 4.1 13.9 - - + -
199C MET* 3.4 18.6 - - + +
256C HIS* 2.8 38.6 + + - -
308C TRP* 4.9 2.9 - + - -
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Residues in contact with THR 80 (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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8C ILE* 3.6 1.4 - - - -
9C ALA* 2.8 45.8 + - - +
33C CSS 4.1 24.2 - - - -
36C THR* 4.6 7.0 - - + +
42C PHE* 4.2 8.7 - - + -
44C GLY 3.6 3.6 - - - -
45C PHE* 4.3 2.9 - - + -
78C GLN* 3.6 9.6 + - + +
79C TYR* 1.3 80.4 - - - +
81C VAL* 1.3 60.6 + - - +
82C TRP* 2.9 32.0 + - + -
88C HIS* 4.0 6.4 + - - -
116C GLU* 4.1 4.3 + - - +
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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
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6C PRO* 3.6 29.4 - - + -
7C ILE 3.4 6.5 - - - +
8C ILE* 4.2 13.9 - - + -
42C PHE* 3.8 4.0 - - - -
43C LEU* 2.8 28.8 + - + -
44C GLY 2.9 17.6 + - - +
45C PHE* 4.7 0.7 - - - +
79C TYR* 4.8 7.6 - - + -
80C THR* 1.3 78.0 - - - +
82C TRP* 1.3 67.8 + - - +
308C TRP* 3.6 55.9 - - + +
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Residues in contact with TRP 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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6C PRO* 3.3 6.2 - - - +
7C ILE* 2.8 39.0 + - + +
9C ALA* 4.4 5.6 - - + -
36C THR* 3.4 34.3 - - + -
39C HIS* 4.1 9.4 - - + -
41C GLY 3.4 15.5 - - - -
42C PHE* 3.7 22.7 - + + -
43C LEU* 3.6 5.6 - - - -
80C THR* 2.9 44.1 + - - -
81C VAL* 1.3 75.7 - - - +
83C LYS* 1.3 61.2 + - - +
84C ASP 3.5 18.2 - - - +
87C SER* 3.6 22.7 - - - -
88C HIS* 3.2 48.2 - + + -
91C MET* 3.7 20.2 - - + -
118C TYR* 5.6 1.8 - + + -
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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