Contacts of the strand formed by residues 75 - 79 (chain B) in PDB entry 2IHU
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 GLN 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLY 5.4 4.4 + - - -
27B VAL* 4.5 18.8 - - - +
28B GLY 4.9 2.4 + - - -
29B LYS 4.7 4.5 + - - +
31B PHE* 5.3 1.3 - - + -
64B ALA* 3.4 24.0 - - + +
67B LEU* 3.6 28.2 - - + +
68B ALA* 3.4 28.0 - - + +
71B THR* 3.3 24.0 + - - +
73B ARG* 3.6 12.3 + - - +
74B PRO* 1.3 84.6 + - - +
76B ALA* 1.3 57.2 + - - +
101B PRO 3.2 5.5 + - - -
102B VAL* 3.5 4.0 - - + -
103B ILE* 2.8 33.9 + - - +
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Residues in contact with ALA 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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22B LEU* 4.3 27.4 - - + -
27B VAL* 4.1 18.4 - - + +
29B LYS 3.9 8.2 + - - +
30B VAL* 3.6 8.5 - - + -
31B PHE* 3.2 31.3 + - - -
64B ALA* 3.8 4.0 - - - +
75B GLN* 1.3 78.6 - - - +
77B CYS* 1.3 60.5 + - - +
102B VAL* 5.1 0.2 - - - -
103B ILE* 3.3 10.3 - - + +
105B LEU* 4.6 4.5 - - + -
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Residues in contact with CYS 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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30B VAL* 4.3 2.5 - - - -
31B PHE 3.0 12.1 - - - +
60B ALA 3.7 20.4 - - - +
61B GLY* 3.9 12.1 - - - +
64B ALA* 4.1 1.8 - - + -
76B ALA* 1.3 75.0 - - - +
78B TRP* 1.3 60.4 + - - +
88B LEU* 3.8 20.0 - - + -
92B ILE* 5.4 2.2 - - - -
102B VAL* 3.8 24.0 - - - -
103B ILE 3.1 7.8 + - - +
104B ALA* 3.8 16.4 - - - -
105B LEU* 3.0 31.4 + - - +
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Residues in contact with TRP 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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18B LEU* 3.7 15.9 - - + -
19B LEU* 5.9 1.1 - - + -
30B VAL* 3.8 15.7 - - + -
31B PHE 2.7 10.2 + - - +
32B GLY* 3.1 19.1 - - - -
33B VAL 3.2 18.4 + - - -
34B VAL* 4.4 5.8 - - + +
37B GLU* 2.9 34.3 + - + +
41B ILE* 3.8 34.8 - - + -
43B PHE* 3.5 27.8 - + - -
51B PHE* 3.9 5.8 - - + -
57B GLU* 4.5 1.2 - - - +
77B CYS* 1.3 76.7 - - - +
79B ALA* 1.3 73.1 + - - +
88B LEU* 4.3 7.5 - - - +
105B LEU* 3.3 28.9 - - + -
107B ALA* 5.0 4.5 - - + -
168B LEU* 3.5 31.6 - - + -
173B LEU* 3.9 9.2 - - + -
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Residues in contact with ALA 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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33B VAL 3.6 6.3 - - - -
57B GLU* 3.7 12.3 - - + -
78B TRP* 1.3 88.6 + - - +
80B THR* 1.3 61.6 - - - +
84B GLY 3.3 30.3 - - - +
85B MET* 3.9 2.7 - - - +
88B LEU* 3.9 15.9 - - + -
105B LEU 3.0 7.4 + - - +
106B ALA* 3.2 3.8 - - + -
107B ALA 3.1 20.8 + - - -
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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