Contacts of the strand formed by residues 29 - 39 (chain B) in PDB entry 4R7X
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 THR 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASP 4.9 2.4 - - - +
16B LEU* 5.2 8.0 - - - +
24B TYR* 3.5 14.1 - - - -
28B ASP* 1.3 71.4 - - - +
30B VAL* 1.3 63.4 + - - +
31B SER* 3.4 18.9 + - - +
115B SER* 3.5 24.7 - - - +
116B PHE 3.7 5.6 - - - +
117B GLU* 2.7 25.2 + - - +
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Residues in contact with VAL 30 (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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13B PHE* 4.2 24.5 - - + -
24B TYR* 3.6 43.7 - - + +
28B ASP 3.6 1.2 + - - +
29B THR* 1.3 69.4 - - - +
31B SER* 1.3 60.1 + - - +
114B PHE* 4.5 1.7 - - + -
115B SER* 3.7 1.0 - - - -
116B PHE* 3.2 61.5 + - + -
118B LEU* 4.2 17.9 - - + -
138B VAL* 4.5 3.1 - - + -
156B PHE* 4.1 17.7 - - + -
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.8 7.6 - - - -
14B ASP* 2.9 43.1 + - - +
24B TYR* 4.5 2.1 + - - -
29B THR* 3.4 15.1 + - - +
30B VAL* 1.3 76.9 - - - +
32B GLY* 1.3 58.8 + - - +
114B PHE* 3.3 21.1 - - - -
115B SER* 3.7 16.4 - - - -
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Residues in contact with GLY 32 (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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12B SER 3.1 13.9 - - - -
14B ASP* 3.5 17.6 + - - -
31B SER* 1.3 76.9 + - - +
33B ARG* 1.3 59.8 + - - -
113B ALA* 3.2 6.1 - - - +
114B PHE* 2.7 43.5 + - - +
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Residues in contact with ARG 33 (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 ILE* 3.8 0.3 - - - -
12B SER* 2.6 64.7 + - - +
14B ASP* 5.0 9.9 - - - +
32B GLY* 1.3 80.6 - - - +
34B VAL* 1.3 58.7 + - - +
35B ASN* 2.8 25.6 - - - +
109B ARG* 4.0 5.3 - - - +
111B GLU* 3.2 41.8 + - + +
112B TYR 3.6 8.7 - - - +
113B ALA* 4.0 6.3 - - + +
114B PHE* 3.7 6.3 - - - -
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Residues in contact with VAL 34 (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 LEU* 4.2 14.1 - - + -
10B THR 3.8 8.5 - - - +
11B ILE* 4.7 4.5 - - + +
33B ARG* 1.3 70.9 - - - +
35B ASN* 1.3 61.0 + - - +
36B LEU* 5.7 0.2 - - + -
47B LEU* 4.2 17.7 - - + -
49B ILE* 3.7 13.9 - - + -
88B LEU* 3.6 22.2 - - + -
112B TYR* 2.8 38.5 + - + +
114B PHE* 3.5 25.1 - - + -
140B ALA* 3.9 24.5 - - + -
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Residues in contact with ASN 35 (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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8B SER* 6.0 0.2 - - - -
9B LEU* 3.4 8.8 - - - +
10B THR* 2.8 47.8 + - - +
12B SER* 3.7 6.6 + - - -
33B ARG* 2.8 51.3 - - - +
34B VAL* 1.3 73.7 - - - +
36B LEU* 1.3 59.8 + - - +
37B GLU 4.2 0.2 - - - -
109B ARG* 2.6 44.0 - - - +
110B HIS 3.4 7.0 - - - +
111B GLU* 3.8 8.7 - - + +
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Residues in contact with LEU 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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6B VAL* 3.7 22.4 - - + -
8B SER 3.7 14.1 - - - +
9B LEU* 3.8 18.4 - - + -
34B VAL 4.8 0.4 - - - +
35B ASN* 1.3 74.7 - - - +
37B GLU* 1.3 55.9 - - - +
38B VAL* 3.9 14.8 - - + +
42B ILE* 4.8 4.5 - - + -
47B LEU* 5.0 8.5 - - + -
89B ILE* 5.7 0.2 - - + -
105B ILE* 4.1 26.2 - - + -
109B ARG* 3.7 1.9 - - - -
110B HIS* 2.7 45.9 + - + +
112B TYR* 4.3 18.4 - - + +
142B LEU* 4.3 24.7 - - + -
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Residues in contact with GLU 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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6B VAL* 3.7 1.9 - - - +
7B LYS* 2.9 63.0 + - + +
8B SER* 2.9 36.8 + - - +
35B ASN 4.2 0.4 - - - -
36B LEU* 1.3 71.4 - - - +
38B VAL* 1.3 67.3 + - - +
108B GLY 3.9 9.6 - - - +
109B ARG* 4.3 29.0 + - + +
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Residues in contact with VAL 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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5B LYS 3.6 9.2 - - - +
6B VAL* 4.7 1.8 - - + -
7B LYS* 4.2 0.9 - - - +
36B LEU* 3.9 21.1 - - + +
37B GLU* 1.3 83.2 - - - +
39B THR* 1.3 79.1 + - - +
40B GLY 4.3 4.5 - - - +
42B ILE* 3.7 43.7 - - + +
105B ILE* 4.3 11.0 - - + -
106B HIS 3.9 17.9 - - - +
107B SER* 3.4 2.1 + - - -
108B GLY* 2.9 34.1 + - - +
110B HIS* 4.8 0.4 - - - +
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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
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4B GLY* 3.6 0.5 - - - -
5B LYS* 3.1 57.0 + - + +
7B LYS* 3.9 32.1 - - + -
38B VAL* 1.3 78.9 - - - +
40B GLY* 1.3 65.1 + - - +
41B GLU 3.5 0.2 + - - -
107B SER* 4.1 3.6 - - - -
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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