Contacts of the strand formed by residues 35 - 43 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS* 4.5 0.7 - - - -
5A ILE* 3.4 10.8 - - + +
7A GLY* 3.7 28.3 - - - +
31A ILE* 3.0 19.5 + - + +
32A PHE* 3.4 28.3 + - - +
34A TYR* 1.3 83.2 - - + +
36A GLU* 1.3 68.3 + - - +
37A LEU* 3.8 13.6 + - + +
340A LEU* 5.0 2.5 - - + -
352A LEU* 4.2 13.5 - - + -
355A PHE* 3.6 38.6 - - + -
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Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LYS* 3.5 36.8 + - + +
5A ILE 2.6 14.9 + - - +
6A SER* 3.6 6.7 - - - +
7A GLY* 2.7 32.9 + - - -
8A GLY 3.9 0.5 + - - -
32A PHE* 5.3 1.0 - - - -
35A VAL* 1.3 76.9 - - - +
37A LEU* 1.3 57.5 + - - +
53B ASN* 2.7 35.2 + - - +
89B LYS* 2.8 36.5 + - - +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLY* 3.6 29.4 - - - -
8A GLY 3.7 11.2 - - - +
10A VAL* 4.0 17.3 - - + -
31A ILE* 4.3 15.3 - - + -
32A PHE* 4.7 10.8 - - + -
35A VAL* 3.8 13.6 + - + +
36A GLU* 1.3 76.0 + - - +
38A ASP* 1.3 59.9 + - - +
39A LEU* 3.0 35.0 + - + +
336A TRP* 4.0 26.9 - - + -
340A LEU* 4.1 9.6 - - + -
51B ALA 4.8 1.4 - - - +
52B THR* 3.6 6.6 - - - +
53B ASN* 2.9 21.7 + - - +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLY* 3.1 28.0 + - - +
9A SER* 4.1 5.9 + - - -
10A VAL 3.4 8.6 + - - -
36A GLU 4.5 0.4 + - - -
37A LEU* 1.3 68.2 - - - +
39A LEU* 1.3 58.4 + - - +
40A HIS* 3.1 24.0 + - - +
52B THR 4.3 0.9 - - - -
53B ASN* 4.7 10.9 + - - +
55B GLN* 3.5 28.8 - - - +
58B LYS* 5.5 4.0 + - - -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.7 18.4 - - + +
12A GLU* 3.8 37.7 - - + +
27A LYS* 5.1 2.9 - - + +
32A PHE* 3.9 29.4 - - + -
37A LEU* 3.0 37.8 + - + +
38A ASP* 1.3 69.1 - - - +
40A HIS* 1.3 61.2 + - - +
41A SER* 3.4 10.0 + - - -
336A TRP* 4.7 4.3 - - + -
51B ALA* 4.4 6.1 - - + +
52B THR* 3.5 42.6 + - + +
55B GLN* 3.6 7.9 - - - +
56B VAL* 4.5 3.1 + - - +
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Residues in contact with HIS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A SER* 2.6 31.8 + - - -
10A VAL 2.9 17.7 + - - +
11A VAL* 3.3 9.7 - - + -
12A GLU 2.8 32.0 + - - +
38A ASP* 3.1 22.1 + - - +
39A LEU* 1.3 70.0 - - - +
41A SER* 1.3 54.3 + - - +
42A TYR* 3.6 20.0 + - + +
63A ALA* 5.0 0.2 - - + -
67A HIS* 3.1 34.3 + + + -
55B GLN* 3.3 30.2 + - - +
56B VAL* 6.4 0.2 - - - +
59B ASP* 2.7 30.9 + - - +
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLU* 2.7 29.1 + - - -
14A GLN* 3.7 17.2 + - - -
39A LEU* 3.4 13.1 + - - +
40A HIS* 1.3 71.2 - - - +
42A TYR* 1.3 72.1 + - - +
42B TYR* 6.0 2.3 - - - -
48B ASN* 5.2 6.9 + - - -
52B THR* 4.4 15.9 - - - -
56B VAL* 5.8 6.0 - - - +
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Residues in contact with TYR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 4.2 3.8 - - + -
12A GLU 2.9 12.3 + - - +
13A MET* 3.2 5.8 - - + -
14A GLN* 2.8 27.3 + - - +
40A HIS* 3.6 26.7 - - + +
41A SER* 1.3 80.1 + - - +
43A ASP* 1.3 61.2 + - - +
44A LEU* 3.5 2.0 + - + -
56A VAL* 4.1 17.5 - - + -
59A ASP* 4.1 19.7 + - + -
60A ALA* 3.9 31.6 - - + -
63A ALA* 3.4 32.7 - - + +
41B SER 6.0 1.8 - - - -
42B TYR* 4.6 25.6 + + - -
59B ASP* 4.0 15.8 + - - +
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLN* 3.6 19.6 - - - +
20A ARG* 3.2 27.0 + - - -
42A TYR* 1.3 70.2 - - - +
44A LEU* 1.3 59.5 + - - +
45A GLY* 2.9 23.7 + - - +
48A ASN* 2.8 46.8 + - - +
56A VAL* 3.5 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