Contacts of the strand formed by residues 74 - 79 (chain B) in PDB entry 1DWQ
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 VAL 74 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B HIS* 3.3 36.8 - - + +
7B VAL* 3.7 26.7 - - + -
64B PHE* 4.3 0.9 - - + -
65B LEU* 3.9 21.8 - - + -
68B LEU* 3.8 17.5 - - + -
72B GLU* 5.9 0.2 - - + -
73B LYS* 1.3 78.4 - - - +
75B ILE* 1.3 63.2 + - - +
76B ILE* 4.0 13.2 + - + -
96B LYS 2.8 16.1 + - - +
97B ILE* 3.6 3.9 - - + +
98B ALA* 2.8 24.7 + - - -
99B ALA 3.8 0.7 + - - +
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Residues in contact with ILE 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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4B ALA* 3.7 28.5 - - + -
5B HIS 3.0 6.4 + - - +
6B PHE* 3.2 32.6 - - + +
7B VAL 3.0 21.6 + - - -
74B VAL* 1.3 77.5 - - - +
76B ILE* 1.3 60.2 + - - +
77B VAL* 3.7 1.9 + - + -
98B ALA* 4.1 14.8 - - + -
99B ALA* 3.4 16.4 - - + +
101B VAL* 3.7 25.4 - - + -
253B VAL* 4.0 10.8 - - + +
254B ALA* 3.7 18.6 - - - +
257B TYR* 5.1 1.1 - - + -
258B ALA 3.7 12.6 - - - +
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Residues in contact with ILE 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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7B VAL* 3.4 10.3 - - + +
9B ILE* 3.9 24.5 - - + -
61B LEU* 4.2 11.0 - - + -
65B LEU* 4.1 17.3 - - + -
74B VAL* 3.9 17.0 - - + -
75B ILE* 1.3 72.2 - - - +
77B VAL* 1.3 55.0 + - - +
86B ILE* 3.8 31.7 - - + +
89B ALA* 4.2 10.8 - - + -
97B ILE* 3.7 36.3 - - + -
99B ALA 3.1 7.7 + - - +
100B GLY* 3.4 2.1 - - - -
101B VAL* 2.7 33.6 + - - +
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Residues in contact with VAL 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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6B PHE* 3.9 28.0 - - + -
7B VAL 3.0 5.5 + - - -
8B LEU* 3.5 20.3 - - + -
9B ILE* 2.7 27.0 + - - +
19B TRP* 4.0 22.1 - - + -
22B LEU* 5.3 0.2 - - + -
75B ILE 4.1 1.1 - - - +
76B ILE* 1.3 76.4 - - - +
78B GLY* 1.3 59.9 + - - +
86B ILE* 4.5 0.4 - - - -
101B VAL* 3.4 29.2 - - + +
103B HIS* 4.4 11.7 - - + -
203B ILE* 5.7 0.9 - - + -
250B LEU* 4.2 16.4 - - + -
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Residues in contact with GLY 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 ILE* 3.3 10.5 - - - -
19B TRP* 4.7 0.7 - - - -
77B VAL* 1.3 74.6 - - - +
79B GLU* 1.3 61.1 + - - -
82B ALA* 3.6 13.7 - - - -
86B ILE* 3.8 12.8 - - - +
101B VAL 2.9 10.9 + - - +
102B PHE* 3.7 0.3 - - - -
103B HIS* 2.9 25.6 + - - -
105B SER* 3.6 8.0 - - - -
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Residues in contact with GLU 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 ILE 3.0 15.3 + - - +
10B HIS* 3.9 0.2 - - - -
11B THR* 3.0 34.5 + - - +
14B HIS* 4.3 0.5 - - - -
18B ILE* 3.6 15.8 - - - +
19B TRP* 3.8 7.8 - - + -
78B GLY* 1.3 74.1 - - - -
80B SER* 1.3 62.8 + - - +
81B CSA 3.1 1.4 + - - -
82B ALA* 2.8 26.8 + - - +
103B HIS* 3.3 25.1 + - - +
105B SER* 4.0 0.4 - - - -
236B HIS* 5.0 2.0 + - + +
237B LYS* 3.0 29.1 + - - +
239B GLN* 2.8 29.7 + - - +
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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