Contacts of the strand formed by residues 5 - 14 (chain C) in PDB entry 6B0Z
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 ILE 5 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C LYS* 1.3 74.7 - - - +
6C SER* 1.3 72.2 + - - +
7C GLY 3.3 0.5 + - - -
34C TYR* 3.0 20.0 + - + +
35C VAL* 3.5 4.1 - - + -
36C GLU* 2.9 27.1 + - - +
349C ASN* 4.8 0.4 - - - +
351C GLU* 3.9 29.2 - - + +
352C LEU* 3.9 35.9 - - + +
354C PHE* 6.1 2.2 - - + -
355C PHE* 4.0 26.2 - - + -
409C LEU* 6.0 4.0 - - + -
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Residues in contact with SER 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LYS 3.6 4.0 + - - -
5C ILE* 1.3 73.9 - - - +
7C GLY* 1.3 58.6 + - - +
8C GLY* 4.6 4.7 + - - -
36C GLU* 3.8 6.0 + - - +
349C ASN* 2.6 35.7 + - - -
352C LEU* 4.4 0.2 - - - +
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Residues in contact with GLY 7 (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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5C ILE 3.3 2.2 + - - -
6C SER* 1.3 73.7 + - - +
8C GLY* 1.3 59.3 + - - +
35C VAL* 3.9 7.6 - - - -
36C GLU 2.7 19.2 + - - -
37C LEU* 3.6 18.8 - - - -
343C ARG* 3.3 12.6 - - - +
347C ASP* 4.3 3.5 - - - +
349C ASN* 4.6 1.4 + - - -
352C LEU* 3.2 28.1 - - - +
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Residues in contact with GLY 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER* 3.7 5.6 + - - -
7C GLY* 1.3 79.8 - - - +
9C SER* 1.3 62.5 + - - -
10C VAL* 3.3 2.8 + - - -
36C GLU 4.0 4.4 + - - -
37C LEU* 3.5 6.1 - - - +
38C ASP* 2.5 36.0 + - - +
343C ARG* 4.3 2.2 - - - -
347C ASP* 4.6 5.6 - - - -
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Residues in contact with SER 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY* 1.3 68.3 - - - -
10C VAL* 1.3 59.9 + - - +
38C ASP* 2.8 27.9 + - - +
40C HIS* 4.3 2.2 - - - -
67C HIS* 3.9 27.6 + - - +
69C VAL* 4.2 2.8 - - - +
343C ARG* 2.5 48.4 + - - +
347C ASP* 5.1 0.6 + - - -
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Residues in contact with VAL 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLY 3.3 0.8 + - - +
9C SER* 1.3 79.5 - - - +
11C VAL* 1.3 75.8 + - - +
37C LEU* 3.7 28.3 - - + -
38C ASP 3.1 7.9 + - - +
39C LEU* 3.4 15.6 - - + +
40C HIS* 2.9 24.0 + - - -
69C VAL* 3.9 22.7 - - + +
71C VAL* 4.2 19.7 - - + -
336C TRP* 5.1 5.8 - - + -
340C LEU* 4.2 13.5 - - + -
343C ARG* 4.1 13.9 - - + -
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Residues in contact with VAL 11 (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 VAL* 1.3 77.0 - - - +
12C GLU* 1.3 66.5 + - - +
13C MET* 4.2 2.9 - - + +
40C HIS* 3.4 17.7 - - + +
42C TYR* 3.9 13.2 - - + -
60C ALA* 4.0 10.8 - - - +
63C ALA* 3.5 40.2 - - + +
64C ILE* 3.9 11.2 - - + +
67C HIS* 3.8 21.3 - - + -
69C VAL 2.9 15.9 + - - +
70C GLY* 3.1 2.6 - - - -
71C VAL 3.0 25.3 + - - -
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Residues in contact with GLU 12 (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 VAL 3.8 1.4 + - - -
11C VAL* 1.3 75.6 - - - +
13C MET* 1.3 71.8 + - - +
14C GLN* 3.6 13.0 + - - +
23C TRP* 2.7 34.2 + - + +
27C LYS* 2.6 37.6 + - - +
39C LEU* 3.9 20.9 - - + +
40C HIS 2.9 8.9 + - - +
41C SER* 3.1 29.4 + - - -
42C TYR* 3.2 20.8 + - - +
71C VAL* 3.6 6.3 - - + +
336C TRP* 4.1 9.2 - - + -
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Residues in contact with MET 13 (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 VAL* 4.2 4.3 - - + +
12C GLU* 1.3 80.1 - - - +
14C GLN* 1.3 62.1 - - - +
23C TRP* 4.0 2.4 - - - -
42C TYR 3.3 4.3 - - - +
44C LEU* 3.8 21.1 - - + -
60C ALA* 3.9 16.2 - - + -
64C ILE* 3.6 34.3 - - + -
70C GLY* 4.1 4.9 - - - -
71C VAL 3.0 41.0 + - - +
72C LYS* 3.6 21.4 - - + -
73C CYS* 2.8 31.0 + - - +
99C ILE* 4.1 22.0 - - - -
304C GLU* 4.3 4.5 - - + +
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Residues in contact with GLN 14 (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 GLU* 3.6 30.7 + - - +
13C MET* 1.3 76.2 - - - +
15C GLY* 1.3 61.1 + - - +
20C ARG* 5.5 6.7 - - + -
23C TRP* 4.4 10.5 - - + +
24C GLU* 4.1 8.7 + - - +
27C LYS* 3.6 13.1 - - - +
41C SER* 4.5 8.6 - - - -
42C TYR 2.9 16.0 + - - +
43C ASP* 3.8 30.0 - - - +
44C LEU* 3.0 28.6 + - - +
45C GLY 4.3 0.9 - - - -
73C CYS* 4.0 3.4 - - - -
75C THR* 4.3 1.7 - - - +
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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