Contacts of the strand formed by residues 5 - 14 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LYS* 1.3 71.1 - - - +
6B SER* 1.3 74.0 + - - +
7B GLY 3.4 0.7 + - - +
34B TYR* 2.9 21.4 + - + +
35B VAL* 3.4 4.2 - - + -
36B GLU* 2.8 30.4 + - - +
349B ASN* 4.6 0.7 - - - +
351B GLU* 3.8 24.5 - - + +
352B LEU* 3.9 32.8 - - + +
354B PHE* 6.5 0.2 - - + -
355B PHE* 3.7 36.6 - - + -
409B LEU* 6.0 1.3 - - + -
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Residues in contact with SER 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LYS 3.4 4.5 + - - -
5B ILE* 1.3 71.5 - - - +
7B GLY* 1.3 54.3 + - - +
8B GLY* 4.6 4.0 + - - -
36B GLU* 4.0 6.7 - - - -
349B ASN* 2.7 32.1 + - - -
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Residues in contact with GLY 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE 3.4 1.4 + - - -
6B SER* 1.3 73.8 + - - +
8B GLY* 1.3 59.9 + - - +
35B VAL* 3.8 9.2 - - - -
36B GLU 2.7 19.7 + - - -
37B LEU* 3.8 14.8 - - - +
343B ARG* 3.3 25.6 - - - +
347B ASP* 4.6 1.7 - - - +
349B ASN* 4.5 3.3 + - - -
352B LEU* 3.5 15.8 - - - +
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Residues in contact with GLY 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B SER* 3.6 5.5 + - - -
7B GLY* 1.3 80.0 - - - +
9B SER* 1.3 59.7 + - - -
10B VAL* 3.6 1.8 + - - -
36B GLU 3.9 3.4 + - - -
37B LEU* 3.6 7.0 - - - +
38B ASP* 2.8 41.8 + - - +
343B ARG* 4.6 1.8 - - - -
347B ASP* 4.8 5.6 - - - -
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Residues in contact with SER 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY* 1.3 70.4 - - - -
10B VAL* 1.3 59.7 + - - +
38B ASP* 3.5 10.5 + - - -
40B HIS* 2.4 36.0 + - - -
67B HIS* 3.1 20.9 + - - +
69B VAL* 4.2 3.6 - - - +
343B ARG* 2.8 47.8 + - - +
347B ASP* 5.1 0.2 + - - -
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY 3.6 1.0 + - - +
9B SER* 1.3 80.1 + - - +
11B VAL* 1.3 70.1 + - - +
37B LEU* 3.7 27.4 - - + -
38B ASP 3.3 6.0 + - - +
39B LEU* 3.6 19.2 - - + +
40B HIS* 2.8 34.8 + - - -
69B VAL* 4.2 17.3 - - + -
71B VAL* 4.1 17.3 - - + -
336B TRP* 4.7 8.3 - - + -
340B LEU* 4.0 15.7 - - + -
343B ARG* 4.3 11.4 - - + -
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Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 1.3 74.1 - - - +
12B GLU* 1.3 60.7 + - - +
13B MET* 4.4 9.2 - - + -
40B HIS* 3.3 17.5 - - + +
42B TYR* 4.0 15.9 - - + -
60B ALA 4.2 2.2 - - - +
63B ALA* 3.5 37.0 - - + +
64B ILE* 3.8 21.3 - - + +
67B HIS* 4.0 13.0 - - + -
69B VAL 2.9 19.4 + - - +
70B GLY* 3.4 3.6 - - - -
71B VAL* 2.9 31.5 + - - +
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL 3.9 0.6 + - - -
11B VAL* 1.3 74.6 - - - +
13B MET* 1.3 61.0 + - - +
14B GLN* 3.6 7.5 - - - +
23B TRP* 2.9 32.9 + - + +
27B LYS* 2.5 38.1 + - - +
39B LEU* 3.9 23.7 - - + +
40B HIS 2.8 7.9 + - - +
41B SER* 2.7 31.0 + - - -
42B TYR* 2.8 33.1 + - - +
71B VAL* 3.4 8.7 - - + -
336B TRP* 3.9 11.7 - - + -
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Residues in contact with MET 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.4 3.8 - - + +
12B GLU* 1.3 79.2 - - - +
14B GLN* 1.3 60.3 + - - +
23B TRP* 4.0 2.6 + - - -
42B TYR* 3.2 5.4 - - + +
44B LEU* 3.9 17.9 - - + -
60B ALA* 3.8 24.0 - - + -
64B ILE* 3.7 35.0 - - + -
70B GLY* 4.2 2.9 - - - -
71B VAL 2.9 44.4 + - - +
72B LYS* 3.7 22.2 - - + -
73B CYS* 2.8 32.4 + - - +
99B ILE* 3.9 22.9 - - - -
304B GLU* 4.4 1.8 - - - +
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Residues in contact with GLN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASN* 5.7 2.6 + - - -
12B GLU* 3.6 16.8 - - - +
13B MET* 1.3 73.7 - - - +
15B GLY* 1.3 60.4 + - - +
20B ARG* 5.7 4.7 - - + -
23B TRP* 4.5 5.8 - - + +
24B GLU* 4.0 12.2 + - - +
27B LYS* 3.5 16.6 - - - +
41B SER* 3.3 20.7 + - - +
42B TYR 2.8 11.8 + - - +
43B ASP* 3.7 32.4 - - - +
44B LEU* 2.9 31.6 + - - +
45B GLY 4.4 0.2 - - - -
73B CYS* 3.9 3.4 - - - -
75B THR* 4.3 0.7 - - - +
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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
------------------------------------------------------------
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