Contacts of the strand formed by residues 73 - 81 (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 ALA 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B PHE 3.1 6.5 + - - -
5B LEU* 3.2 8.8 - - + +
6B MET* 2.8 23.0 + - - +
62B PHE* 3.5 34.3 - - + -
66B THR* 3.7 21.5 - - + +
67B ALA* 3.9 9.4 - - + +
71B ALA 3.9 0.6 + - - -
72B PRO* 1.3 72.3 - - - +
74B THR* 1.3 61.1 + - - +
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Residues in contact with THR 74 (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* 3.2 33.9 - - - +
8B ARG* 4.0 22.8 + - + +
45B TYR 4.4 2.4 - - - +
46B LYS* 4.8 6.1 - - - +
47B ASP 5.0 2.9 + - - -
62B PHE* 4.1 10.4 - - - -
72B PRO 3.9 0.8 + - - -
73B ALA* 1.3 73.4 - - - +
75B VAL* 1.3 72.6 + - - +
76B GLY 4.3 2.3 + - - +
90B ILE* 4.6 11.7 - - + -
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Residues in contact with VAL 75 (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* 4.0 31.2 - - + -
6B MET 2.9 10.3 + - - +
7B ILE* 3.2 10.9 - - + +
8B ARG 2.8 26.9 + - - -
27B LEU* 4.6 7.9 - - + -
44B LEU* 4.0 28.5 - - + -
45B TYR 3.4 12.6 - - - +
51B LEU* 4.6 5.6 - - + -
62B PHE* 3.6 23.6 - - + -
73B ALA 4.5 0.7 - - - +
74B THR* 1.3 76.9 - - - +
76B GLY* 1.3 71.5 + - - +
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Residues in contact with GLY 76 (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 3.6 7.0 - - - -
44B LEU* 3.4 10.4 - - - +
45B TYR* 2.8 41.7 + - - -
47B ASP 5.3 2.3 + - - +
74B THR* 4.1 3.8 + - - +
75B VAL* 1.3 75.3 - - - +
77B LEU* 1.3 59.7 + - - -
88B LEU* 4.1 8.1 - - - -
90B ILE* 4.0 15.9 - - - -
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Residues in contact with LEU 77 (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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7B ILE* 3.9 19.3 - - + -
8B ARG 2.9 13.7 + - - +
9B ARG* 3.4 33.0 - - + +
14B ILE* 5.6 0.4 - - + -
31B VAL* 4.0 10.1 - - + -
35B LEU* 4.0 27.8 - - + -
42B GLN* 3.8 26.5 - - + +
43B ARG 3.3 15.0 - - - +
44B LEU* 3.6 13.7 - - + -
76B GLY* 1.3 74.6 - - - +
78B ALA* 1.3 66.1 + - - +
79B PHE* 4.0 18.2 - - + -
86B GLU* 4.4 0.7 - - - +
88B LEU* 3.8 13.1 - - - +
89B CYS 5.0 1.7 + - - +
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Residues in contact with ALA 78 (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 ARG* 4.8 0.2 - - - +
42B GLN* 3.4 4.2 - - - -
43B ARG* 2.9 37.1 + - + -
45B TYR* 4.0 22.2 - - + +
77B LEU* 1.3 74.6 - - - +
79B PHE* 1.3 65.9 + - - +
85B PHE* 3.8 3.6 - - + -
86B GLU* 3.5 33.4 - - + +
88B LEU* 4.2 10.1 - - - -
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Residues in contact with PHE 79 (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 ARG* 3.2 39.7 - - - +
31B VAL* 5.0 1.6 - - + -
35B LEU* 3.8 33.0 - - + -
37B ARG* 3.5 56.3 - - + +
41B GLU 3.4 13.5 - - - +
42B GLN* 4.0 13.5 - - + -
77B LEU* 4.0 17.5 - - + -
78B ALA* 1.3 77.1 - - - +
80B ARG* 1.3 62.5 + - - +
81B ALA 3.5 0.5 + - - -
85B PHE* 3.5 4.5 - - - -
86B GLU* 3.0 41.8 + - - +
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Residues in contact with ARG 80 (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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37B ARG* 3.1 24.5 + - - +
40B ASP* 3.1 40.0 + - - +
41B GLU* 3.1 27.3 + - + +
79B PHE* 1.3 72.5 - - - +
81B ALA* 1.3 58.2 + - - +
82B ASP 3.4 25.7 + - - +
83B ASP* 3.9 14.1 + - - +
84B THR 3.6 12.6 - - - +
85B PHE* 3.3 35.7 - - + -
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Residues in contact with ALA 81 (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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37B ARG* 5.3 0.7 - - - +
79B PHE 3.5 3.5 + - - +
80B ARG* 1.3 69.0 - - - +
82B ASP* 1.3 68.7 + - - +
84B THR* 2.7 36.8 + - + +
85B PHE* 4.2 0.2 - - - +
86B GLU* 4.7 15.0 - - + +
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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