Contacts of the strand formed by residues 91 - 98 (chain A) in PDB entry 4ZXB
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 ALA 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG* 4.0 10.8 - - + -
39A GLN 3.5 26.7 - - - +
40A PRO* 3.6 6.5 - - + -
41A PRO* 4.3 4.5 - - - -
89A ASP 3.2 10.6 + - - +
90A THR* 1.3 77.2 - - - +
92A ARG* 1.3 62.9 + - - +
93A TYR* 3.3 16.5 - - + -
113A SER* 4.7 0.9 - - - -
114A VAL 2.9 30.1 + - - +
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Residues in contact with ARG 92 (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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37A VAL 4.0 0.3 - - - +
38A ARG* 3.2 4.9 - - - +
39A GLN* 2.8 37.8 + - + +
91A ALA* 1.3 73.7 - - - +
93A TYR* 1.3 62.9 + - - +
94A TYR* 3.3 32.6 + - + +
110A GLN* 2.8 35.5 + - - +
111A GLY* 3.2 16.6 + - - -
112A THR 3.3 13.0 - - - +
113A SER* 2.8 36.5 + - - +
154A PRO* 4.8 6.7 - - - +
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Residues in contact with TYR 93 (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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6A GLU* 3.7 3.8 - - - +
18A LEU* 3.8 17.2 - - + +
20A ILE* 3.7 20.2 - - + -
36A TRP* 4.8 4.7 - + + -
37A VAL 3.7 2.9 - - - +
38A ARG* 3.0 32.5 + - + -
48A LEU* 3.8 22.9 - - + -
80A LEU* 3.9 14.8 - - + -
82A MET* 3.9 12.5 - - + -
89A ASP* 2.7 34.5 + - - +
91A ALA* 3.3 24.9 - - + -
92A ARG* 1.3 73.4 - - - +
94A TYR* 1.3 60.4 + - - +
111A GLY* 3.4 1.4 - - - -
112A THR* 2.7 41.5 + - + +
114A VAL* 3.7 20.6 - - + -
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Residues in contact with TYR 94 (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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6A GLU* 3.1 6.1 - - - +
35A ASN 3.8 0.2 - - - +
36A TRP* 3.3 11.0 - - - -
37A VAL* 2.8 49.0 + - + +
38A ARG* 4.8 0.2 - - - -
39A GLN* 3.3 33.4 + - + -
45A LEU* 4.5 4.3 - - + -
92A ARG* 3.3 34.4 + - + +
93A TYR* 1.3 76.1 - - - +
95A CYS* 1.3 60.2 + - - +
96A ALA* 5.7 0.2 - - + -
108A TRP* 3.7 31.9 - + + -
109A GLY 3.5 18.2 - - - -
110A GLN 3.7 10.1 - - - -
111A GLY* 3.5 7.9 - - - -
44B GLN* 3.5 12.5 + - - -
48B GLN 4.3 3.3 + - - -
49B SER* 3.2 24.5 - - - -
50B PRO* 4.4 1.6 - - + -
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Residues in contact with CYS 95 (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 LEU* 3.8 13.8 - - - +
5A LYS 4.4 0.9 - - - -
6A GLU* 2.9 24.3 + - - -
22A CYS* 2.1 55.4 - - + -
34A VAL* 3.9 7.6 - - + -
35A ASN 3.1 9.6 - - - +
36A TRP* 3.9 11.0 - - + -
94A TYR* 1.3 76.0 - - - +
96A ALA* 1.3 59.7 + - - +
109A GLY 2.9 25.1 + - - -
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Residues in contact with ALA 96 (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 LEU* 3.9 4.7 - - - -
34A VAL* 3.3 2.9 - - - -
35A ASN* 2.8 42.5 + - + +
37A VAL* 5.6 1.6 - - + -
94A TYR 4.2 0.4 - - - -
95A CYS* 1.3 75.4 - - - +
97A ARG* 1.4 62.9 + - - +
105A MET* 4.0 25.6 - - + -
107A TYR 3.2 11.4 - - - +
108A TRP* 3.8 28.5 - - + -
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Residues in contact with ARG 97 (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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2A VAL* 3.6 20.8 - - - +
4A LEU* 3.6 8.4 - - + +
27A PHE* 3.6 38.0 - - + +
32A TYR* 3.3 58.4 + - + -
33A GLY 3.5 4.9 - - - +
34A VAL* 4.7 0.9 - - - +
96A ALA* 1.4 69.7 - - - +
98A ASP* 1.3 62.3 + - - +
99A PRO* 3.3 2.3 - - + +
105A MET* 3.1 5.9 - - - -
106A ASP* 3.0 63.8 + - - +
107A TYR* 2.8 44.8 + - + +
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Residues in contact with ASP 98 (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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32A TYR* 4.0 1.7 - - - -
33A GLY 2.7 32.5 + - - +
35A ASN* 2.9 25.7 + - - +
50A MET* 3.6 10.7 - - + +
97A ARG* 1.3 72.6 - - - +
99A PRO* 1.4 52.4 - - - +
100A TYR* 2.7 36.7 + - - +
103A LYS 4.1 3.1 - - - +
104A PRO* 4.1 1.5 - - - +
105A MET* 3.4 19.5 + - - +
101B ARG* 2.7 43.9 + - - -
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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