Contacts of the strand formed by residues 36 - 45 (chain B) in PDB entry 4ZR2
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 LEU 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A PHE* 3.8 31.2 - - + -
60A TRP* 5.3 3.6 - - + -
10B MET* 4.4 7.8 - - - +
13B ASN* 4.4 9.0 + - - -
16B PHE* 5.9 1.3 - - + -
32B ILE* 5.8 0.2 - - + -
33B ALA* 3.5 32.7 - - + +
34B VAL 3.4 4.4 - - - +
35B ARG* 1.3 80.2 - - - +
37B THR* 1.3 62.6 + - - +
38B GLN* 3.6 19.9 + - - +
55B SER* 4.1 11.7 - - - -
56B THR 3.4 11.7 - - - +
57B PHE* 3.4 46.0 - - + -
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Residues in contact with THR 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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9B GLU* 3.6 22.2 - - - +
10B MET* 3.6 26.1 - - + +
35B ARG 4.0 0.9 + - - -
36B LEU* 1.3 75.9 + - - +
38B GLN* 1.3 65.8 + - - +
54B THR 3.8 0.2 - - - +
55B SER* 3.4 3.3 - - - -
56B THR* 2.8 39.5 + - - -
58B ARG* 3.6 40.0 + - - +
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Residues in contact with GLN 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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60A TRP* 4.0 5.8 - - - -
128A GLN* 4.7 7.9 - - - +
130A PHE* 3.9 11.3 - - + -
9B GLU* 3.5 3.0 - - - +
10B MET* 2.9 57.9 + - + +
13B ASN* 5.7 2.1 - - - +
16B PHE* 5.5 9.8 - - + -
33B ALA 5.4 0.4 + - - -
36B LEU* 3.6 33.7 + - - +
37B THR* 1.3 79.9 - - - +
39B THR* 1.3 64.2 + - - +
53B THR* 3.6 23.9 - - + +
54B THR 3.5 0.9 - - - -
55B SER* 3.3 23.5 - - - -
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Residues in contact with THR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LYS* 4.8 3.9 - - - -
7B THR* 3.9 24.9 - - + -
8B TRP 3.4 8.3 - - - +
9B GLU* 2.6 33.4 + - - +
38B GLN* 1.3 73.1 - - - +
40B LEU* 1.3 63.9 - - - +
41B VAL* 4.0 6.0 - - + +
52B LYS 3.6 1.7 - - - +
53B THR* 3.3 6.9 - - - +
54B THR* 2.9 50.6 + - + +
56B THR* 5.2 6.1 + - - +
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Residues in contact with LEU 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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108A LYS* 4.1 4.5 - - - +
115A LEU* 4.3 17.5 - - + -
117A LEU* 5.0 2.5 - - + -
130A PHE* 4.2 19.1 - - + -
201A RET 4.0 36.6 - - + -
8B TRP* 2.7 52.8 + - + +
38B GLN 4.3 0.2 - - - -
39B THR* 1.3 73.0 - - - +
41B VAL* 1.3 61.8 + - - +
42B ILE* 3.9 27.6 - - + -
51B THR* 4.3 9.0 - - - -
52B LYS 3.8 2.9 - - - +
53B THR* 3.4 23.8 - - + +
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Residues in contact with VAL 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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6B GLY 3.5 6.1 - - - +
7B THR* 3.8 29.6 - - + +
39B THR* 4.7 6.3 - - + -
40B LEU* 1.3 73.2 - - - +
42B ILE* 1.3 68.5 + - - +
43B ASP* 5.0 4.0 - - + +
50B LYS 3.9 0.9 - - - +
51B THR* 3.2 5.7 - - - -
52B LYS* 2.9 54.2 + - + +
54B THR* 5.9 4.7 - - + -
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Residues in contact with ILE 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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108A LYS* 4.3 11.4 - - + +
115A LEU* 3.8 16.4 - - + -
4B GLN* 3.4 38.1 - - + +
5B ASN* 3.3 5.9 - - - +
6B GLY 3.0 27.0 + - - +
8B TRP* 3.8 17.3 - - + +
40B LEU* 3.9 22.2 - - + -
41B VAL* 1.3 82.4 - - - +
43B ASP* 1.3 61.1 + - - +
44B GLN* 4.1 7.2 - - + -
49B PHE* 4.0 27.8 - - + -
50B LYS 3.8 2.0 - - - -
51B THR* 4.2 9.2 - - + +
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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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5B ASN* 3.5 6.4 - - - +
41B VAL* 4.2 4.9 + - + +
42B ILE* 1.3 73.2 - - - +
44B GLN* 1.3 62.5 + - - +
48B ASN 3.9 1.0 - - - +
49B PHE* 3.7 0.5 - - - -
50B LYS* 2.8 71.1 + - + +
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Residues in contact with GLN 44 (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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88A TRP* 3.9 4.8 - - - -
2B ARG* 2.9 23.6 + - - +
3B ASP* 4.3 3.7 - - - +
4B GLN* 2.7 29.4 + - - -
5B ASN* 2.9 33.0 + - - +
42B ILE* 4.1 3.6 - - + -
43B ASP* 1.3 77.1 - - - +
45B ASP* 1.3 62.2 + - - +
46B GLY* 3.2 26.9 + - - +
48B ASN 3.4 4.0 - - - +
49B PHE* 3.3 42.6 - - + +
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Residues in contact with ASP 45 (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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43B ASP 4.3 0.2 + - - -
44B GLN* 1.3 72.5 - - - +
46B GLY* 1.3 61.8 + - - +
47B ASP 3.1 0.7 + - - -
48B ASN* 2.9 47.2 + - + +
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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