Contacts of the strand formed by residues 35 - 43 (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 VAL 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LYS* 4.5 0.2 - - - -
5B ILE* 3.4 17.5 - - + +
7B GLY* 3.8 9.4 - - - -
31B ILE* 3.0 20.1 + - + +
32B PHE* 3.4 24.7 - - - +
34B TYR* 1.3 84.7 - - - +
36B GLU* 1.3 69.8 + - - +
37B LEU* 3.7 31.2 + - + +
340B LEU* 5.1 1.8 - - + -
352B LEU* 4.2 12.8 - - + -
355B PHE* 3.8 39.3 - - + -
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Residues in contact with GLU 36 (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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53A ASN* 3.4 14.6 + - - +
89A LYS* 2.9 44.9 + - - +
4B LYS* 3.9 36.6 + - + +
5B ILE 2.8 13.3 + - - +
6B SER* 4.0 3.6 - - - -
7B GLY* 2.7 31.9 + - - -
8B GLY 3.9 0.7 + - - -
32B PHE* 5.2 0.7 - - - +
35B VAL* 1.3 76.6 - - - +
37B LEU* 1.3 59.5 + - - +
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Residues in contact with LEU 37 (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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51A ALA 4.8 1.0 - - - +
52A THR 3.6 6.2 - - - +
53A ASN* 2.7 27.2 + - - +
7B GLY* 3.8 14.1 - - - -
8B GLY 3.6 4.3 - - - +
10B VAL* 3.7 26.5 - - + -
31B ILE* 4.2 15.5 - - + -
32B PHE* 4.8 10.8 - - + -
35B VAL* 3.7 25.5 + - + +
36B GLU* 1.3 74.3 - - - +
38B ASP* 1.3 60.8 + - - +
39B LEU* 3.0 32.5 + - + +
336B TRP* 4.1 26.9 - - + -
340B LEU* 4.1 9.9 - - + -
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Residues in contact with ASP 38 (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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52A THR 4.2 1.3 - - - -
53A ASN* 4.5 12.1 + - - +
55A GLN* 3.3 30.8 - - - +
58A LYS* 5.7 3.0 + - - -
8B GLY* 2.8 29.1 + - - +
9B SER* 4.1 6.6 + - - -
10B VAL 3.3 20.4 + - - -
37B LEU* 1.3 69.4 - - - +
39B LEU* 1.3 61.0 + - - +
40B HIS* 3.4 8.1 - - - -
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Residues in contact with LEU 39 (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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51A ALA* 4.3 8.3 - - + +
52A THR* 3.6 34.9 + - + +
55A GLN* 3.5 15.5 - - - +
56A VAL* 4.5 3.5 + - - +
10B VAL* 3.6 18.6 - - + +
12B GLU* 3.9 36.8 - - + +
27B LYS* 5.1 3.6 - - + +
32B PHE* 3.9 30.7 - - + -
37B LEU* 3.0 33.1 + - + +
38B ASP* 1.3 69.2 - - - +
40B HIS* 1.3 58.8 + - - +
41B SER* 3.5 10.4 + - - -
336B TRP* 4.7 3.8 - - + -
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Residues in contact with HIS 40 (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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55A GLN* 3.3 32.6 + - - +
59A ASP* 2.8 29.5 + - - +
9B SER* 2.4 30.7 + - - -
10B VAL 2.8 24.2 + - - +
11B VAL* 3.3 12.2 - - + -
12B GLU 2.8 26.4 + - - +
38B ASP* 3.4 11.4 + - - +
39B LEU* 1.3 68.4 - - - +
41B SER* 1.3 58.8 + - - +
42B TYR* 3.4 18.5 - - + +
63B ALA* 4.9 0.2 - - + -
67B HIS* 3.1 36.3 + + + -
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Residues in contact with SER 41 (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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42A TYR* 6.0 1.9 - - - -
48A ASN* 5.2 6.7 + - - -
52A THR* 4.4 14.6 - - - -
56A VAL* 5.7 5.8 - - - +
12B GLU* 2.7 30.0 + - - -
14B GLN* 3.3 18.9 + - - -
27B LYS* 4.9 0.2 + - - -
39B LEU* 3.5 14.4 + - - -
40B HIS* 1.3 72.4 - - - +
42B TYR* 1.3 66.7 + - - +
43B ASP 4.4 0.3 + - - -
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Residues in contact with TYR 42 (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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41A SER 6.0 2.0 - - - -
42A TYR* 4.6 24.3 + + - -
59A ASP* 4.1 13.9 + - - +
11B VAL* 4.0 10.3 - - + -
12B GLU 2.8 11.2 + - - +
13B MET* 3.2 5.2 - - + +
14B GLN* 2.8 26.7 + - - +
40B HIS* 3.4 27.1 - - + -
41B SER* 1.3 79.0 + - - +
43B ASP* 1.3 59.1 + - - +
44B LEU* 3.4 3.4 + - + -
56B VAL* 4.1 18.6 - - + -
59B ASP* 4.0 22.8 + - + +
60B ALA* 3.9 28.0 - - + -
63B ALA* 3.3 33.9 - - + +
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Residues in contact with ASP 43 (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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14B GLN* 3.7 29.4 - - - +
15B GLY 4.8 1.0 - - - +
41B SER 4.4 0.2 + - - -
42B TYR* 1.3 69.3 - - - +
44B LEU* 1.3 59.2 + - - +
45B GLY* 2.9 27.2 + - - -
48B ASN* 3.0 42.1 + - - +
56B VAL* 3.6 13.0 - - - +
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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