Contacts of the strand formed by residues 2 - 9 (chain B) in PDB entry 2IZV
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 ASP 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 75.4 + - - +
3B VAL* 1.3 66.3 + - - +
4B PHE* 3.7 32.8 - - + -
17B ASP* 4.4 11.6 - - + +
18B ALA* 3.5 10.4 - - - +
19B LYS* 3.4 22.7 - - - +
64B SER* 5.2 6.8 + - - -
67B ALA 4.6 1.0 - - - +
82C ARG* 5.8 4.4 - - - +
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Residues in contact with VAL 3 (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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1B MET* 5.0 0.7 - - + -
2B ASP* 1.3 78.9 - - - +
4B PHE* 1.3 62.6 + - - +
5B LEU* 4.4 8.7 - - + +
17B ASP* 3.1 6.9 - - - +
18B ALA 2.8 42.0 + - - +
19B LYS 4.5 2.7 - - - +
20B GLU* 4.1 17.9 - - + +
57B LEU* 4.2 24.0 - - + -
62B PHE* 3.7 30.1 - - + +
63B THR* 3.9 19.1 - - - -
64B SER 4.4 0.4 - - - +
67B ALA* 3.7 14.6 - - + -
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Residues in contact with PHE 4 (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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2B ASP* 3.7 33.9 - - + -
3B VAL* 1.3 73.7 - - - +
5B LEU* 1.3 61.8 + - - +
16B THR 3.8 3.4 - - - +
17B ASP* 3.5 29.2 - - + -
67B ALA* 2.9 28.8 + - - +
68B ARG 3.6 13.0 - - - +
69B PRO* 3.5 32.3 - - + +
72B PRO* 3.3 7.6 - - + +
73B ALA 3.1 20.1 + - - -
35C HIS* 6.1 0.4 - - - -
78C THR* 3.6 29.8 - - + -
82C ARG* 3.9 23.1 - - + -
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Residues in contact with LEU 5 (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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3B VAL* 4.4 9.4 - - + +
4B PHE* 1.3 83.7 - - - +
6B MET* 1.3 62.1 + - - +
7B ILE* 4.8 2.7 - - + -
14B ILE 3.5 1.6 - - - +
15B PHE* 3.6 5.7 - - - -
16B THR* 2.9 40.8 + - + +
18B ALA* 5.3 2.5 - - + +
27B LEU* 3.8 39.5 - - + -
57B LEU* 4.4 14.4 - - + -
62B PHE* 4.0 20.4 - - + -
67B ALA* 4.3 4.5 - - + -
72B PRO* 3.8 7.3 - - - +
73B ALA* 3.2 25.6 - - + +
75B VAL* 4.0 13.9 - - + -
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Residues in contact with MET 6 (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 LEU* 1.3 70.8 - - - +
7B ILE* 1.3 62.8 + - - +
8B ARG* 3.8 12.0 - - + +
13B THR* 3.8 17.3 - - + -
14B ILE 3.2 4.9 - - - -
15B PHE* 3.4 42.4 - - + -
72B PRO* 3.9 21.8 - - + +
73B ALA 2.8 9.0 + - - +
74B THR* 3.2 24.9 - - - +
75B VAL 2.9 25.2 + - - +
93B PHE* 4.9 12.8 - - + -
75C MET* 3.8 23.8 - - + -
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Residues in contact with ILE 7 (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 LEU* 4.8 5.2 - - + -
6B MET* 1.3 73.5 - - - +
8B ARG* 1.3 63.0 + - - +
12B THR* 3.8 1.6 - - - +
13B THR* 3.3 3.5 - - - -
14B ILE* 2.8 52.7 + - + +
16B THR* 4.5 13.9 - - + -
27B LEU* 4.1 28.5 - - + -
30B ILE* 5.8 1.1 - - + -
31B VAL* 3.4 28.5 - - + -
44B LEU* 4.2 10.3 - - + -
75B VAL* 3.2 19.1 - - + +
77B LEU* 3.9 30.3 - - + -
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Residues in contact with ARG 8 (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 MET* 3.8 16.0 - - - +
7B ILE* 1.3 80.5 - - - +
9B ARG* 1.3 59.9 + - - +
10B HIS 4.8 2.2 + - - +
12B THR 3.3 5.1 + - - +
13B THR* 3.4 25.9 + - + -
74B THR* 4.0 25.2 + - + +
75B VAL 2.8 11.2 + - - +
76B GLY* 3.6 4.5 - - - -
77B LEU* 2.9 25.3 + - - -
90B ILE* 3.4 38.5 - - + +
91B GLU 3.0 27.7 + - - -
92B PRO* 4.4 4.2 - - - +
93B PHE* 3.4 43.0 - - - -
27C HIS* 3.8 4.0 - - - -
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Residues in contact with ARG 9 (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 ARG* 1.3 74.0 - - - +
10B HIS* 1.3 98.7 + - + +
11B LYS 3.1 0.7 + - - -
12B THR* 2.9 34.6 + - + +
35B LEU* 5.6 2.2 - - + -
77B LEU* 3.4 32.8 - - + +
79B PHE* 3.2 45.5 - - - +
86B GLU* 2.7 38.8 + - - +
89B CYS 4.0 4.7 - - - -
90B ILE* 4.5 0.4 - - - +
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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