Contacts of the strand formed by residues 23 - 30 (chain B) in PDB entry 4Q95
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 ARG 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ASP* 4.9 10.9 + - - -
50A GLU* 5.3 6.3 + - - -
62A LEU 5.0 0.2 + - - -
63A LEU* 6.2 0.8 - - - +
122A SER* 2.9 45.0 + - - +
126A GLU* 4.6 4.9 + - - -
201A SHV 3.9 1.4 - - - +
16B GLU* 2.7 41.3 + - + +
17B ILE 3.3 5.6 - - - +
18B PHE* 3.8 30.3 - - + -
19B ARG 5.8 0.2 - - - +
22B TYR* 1.3 84.6 - - - +
24B HIS* 1.3 60.3 + - - +
25B TRP* 3.7 22.9 + - - +
91B LYS* 5.4 3.2 - - - +
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Residues in contact with HIS 24 (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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201A SHV 3.5 23.8 - - + +
15B ILE 3.7 0.2 - - - +
16B GLU* 3.8 0.3 - - - -
17B ILE* 2.8 52.2 + - + +
19B ARG* 3.8 29.2 + - + +
22B TYR* 3.3 27.6 + - + -
23B ARG* 1.3 72.7 - - - +
25B TRP* 1.3 77.1 + - - +
26B ALA* 5.0 0.2 - - + -
36B HIS* 3.0 34.9 + + + -
37B LEU 4.2 6.4 + - - -
39B PRO* 4.3 10.8 - - + -
80B VAL* 4.4 2.2 - - + +
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Residues in contact with TRP 25 (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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122A SER* 3.5 24.2 + - - -
125A CYS* 4.0 22.0 - - + +
126A GLU* 3.5 35.4 + - + +
129A VAL* 4.1 20.2 - - + +
201A SHV 3.1 10.1 + - - +
14B LEU* 4.0 14.4 - - + -
15B ILE 3.4 18.2 - - - -
16B GLU* 3.7 32.4 - - + +
23B ARG* 3.7 24.8 + - - +
24B HIS* 1.3 91.8 + - - +
26B ALA* 1.3 60.5 + - - +
36B HIS* 3.5 9.5 - - - +
37B LEU 4.7 2.4 + - - -
89B ASN* 3.7 41.3 - - + -
91B LYS* 4.0 14.1 - - + -
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Residues in contact with ALA 26 (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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129A VAL* 3.6 12.2 - - - +
14B LEU* 3.6 4.5 - - - +
15B ILE* 2.9 39.5 + - + +
17B ILE* 4.7 12.3 - - + -
24B HIS* 5.0 0.7 - - + -
25B TRP* 1.3 76.1 - - - +
27B ILE* 1.3 60.6 + - - +
34B VAL* 3.9 20.4 - - + -
35B VAL 3.5 7.6 - - - +
36B HIS* 3.8 15.7 - - + -
80B VAL* 5.3 0.2 - - + -
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Residues in contact with ILE 27 (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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129A VAL* 4.0 9.0 - - + +
132A LEU* 3.9 37.2 - - + -
133A ARG 4.0 2.9 - - - +
12B GLY* 3.7 13.5 - - - +
13B ASP 3.5 10.8 - - - +
14B LEU* 3.6 21.3 - - + -
26B ALA* 1.3 74.8 - - - +
28B TYR* 1.3 65.8 + - - +
29B VAL* 3.8 3.0 - - + +
34B VAL* 3.1 5.7 - - - -
35B VAL* 2.8 54.6 + - + +
104B ILE* 3.7 27.4 - - + -
108B ALA* 4.2 7.6 - - + -
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Residues in contact with TYR 28 (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 GLU* 2.6 36.9 + - + +
9B PRO* 3.5 37.0 - - + -
10B LYS 3.4 31.6 - - - +
11B PRO* 3.8 2.9 - - + -
12B GLY* 2.8 26.9 + - - -
13B ASP 2.9 15.1 + - - +
15B ILE* 4.3 4.6 - - + +
27B ILE* 1.3 73.8 - - - +
29B VAL* 1.3 61.3 + - - +
30B GLY* 3.6 19.3 - - - -
31B ASP 3.8 0.7 + - - -
32B GLY* 3.0 36.2 + - - -
33B TYR 3.6 13.5 - - - -
34B VAL* 3.9 13.1 - - + +
77B LEU* 4.4 10.8 - - + -
105B ILE* 4.1 0.7 - - - +
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Residues in contact with VAL 29 (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 PRO* 4.7 3.3 - - - +
27B ILE* 3.8 9.2 - - + +
28B TYR* 1.3 78.2 - - - +
30B GLY* 1.3 59.3 + - - +
33B TYR* 2.9 36.3 + - + +
35B VAL* 3.8 27.1 - - + -
74B LYS* 4.2 6.3 - - - +
104B ILE* 6.3 0.2 - - + -
105B ILE* 3.9 34.9 - - + +
108B ALA* 3.9 19.3 - - + -
109B GLU* 3.6 24.0 - - - +
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Residues in contact with GLY 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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11B PRO* 4.9 8.9 - - - +
28B TYR* 3.6 17.6 - - - -
29B VAL* 1.3 82.4 - - - +
31B ASP* 1.3 73.1 + - - +
32B GLY 3.2 2.7 - - - -
33B TYR* 2.9 23.8 + - - +
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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