Contacts of the strand formed by residues 71 - 76 (chain G) in PDB entry 2QXU
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 71 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4G ASN* 4.0 0.4 - - - -
5G PRO* 3.3 15.0 - - + +
7G VAL* 4.1 13.9 - - + -
59G VAL* 3.7 24.2 - - + -
62G VAL* 4.0 23.1 - - + -
63G LEU* 3.5 24.2 - - + -
70G LYS* 1.3 74.8 - - - +
72G ASP* 1.3 69.8 + - - +
73G ILE* 4.3 11.2 - - + -
95G LYS 2.9 15.6 + - - +
96G VAL* 3.2 8.1 - - + +
97G ALA 2.9 22.7 + - - -
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Residues in contact with ASP 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G HIS* 5.5 0.5 - - - -
4G ASN* 3.0 37.0 + - - +
5G PRO 2.9 9.8 + - - +
6G VAL* 3.4 9.3 - - + +
7G VAL* 2.8 26.3 + - - +
31G TRP* 5.5 1.4 + - - -
71G VAL* 1.3 74.6 - - - +
73G ILE* 1.3 63.5 + - - +
97G ALA* 3.2 1.4 - - - +
98G ASN* 2.9 49.2 + - - +
173G LEU* 3.5 28.8 - - + +
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Residues in contact with ILE 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G VAL* 3.2 20.6 - - + +
9G VAL* 4.0 7.6 - - + -
55G LEU* 5.0 4.5 - - + -
59G VAL* 4.9 5.6 - - + -
71G VAL* 4.3 7.9 - - + -
72G ASP* 1.3 80.8 - - - +
74G VAL* 1.3 76.6 + - - +
75G ALA* 4.1 2.5 - - + +
83G THR* 3.6 41.7 - - + +
86G TYR* 4.5 13.0 - - + -
96G VAL* 3.9 26.9 - - + +
98G ASN 2.8 12.2 + - - +
99G VAL* 3.4 10.4 - - + -
100G VAL* 2.8 28.2 + - - +
173G LEU* 4.5 1.1 - - - +
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Residues in contact with VAL 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G VAL* 3.8 20.2 - - + -
7G VAL 3.1 4.4 + - - -
8G MET* 3.2 14.4 - - + +
9G VAL 2.8 23.2 + - - -
19G PHE* 4.0 13.3 - - + -
22G ILE* 4.9 6.3 - - + -
26G LEU* 5.2 0.4 - - + -
73G ILE* 1.3 79.5 - - - +
75G ALA* 1.3 61.8 + - - +
100G VAL* 3.2 10.3 - - + +
102G LEU* 4.0 26.2 - - + -
169G ILE* 4.2 23.1 - - + -
173G LEU* 3.9 22.0 - - + -
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Residues in contact with ALA 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL* 3.3 8.5 - - + +
19G PHE* 4.8 1.1 - - - -
73G ILE* 4.0 3.1 - - + -
74G VAL* 1.3 74.8 - - - +
76G HIS* 1.3 54.7 + - - +
79G GLY 3.5 29.6 - - - +
80G GLY* 3.6 9.0 - - - +
83G THR* 3.5 14.6 - - + +
100G VAL 2.8 12.0 + - - +
101G THR* 3.2 6.9 - - + -
102G LEU* 2.7 36.3 + - - +
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Residues in contact with HIS 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G VAL 2.9 9.8 + - - +
10G HIS* 4.8 0.2 - - - -
11G GLY* 3.4 17.7 + - - +
18G ASN* 5.5 3.2 + - - +
19G PHE* 4.1 10.3 - - + -
75G ALA* 1.3 74.6 - - - +
77G SER* 1.3 64.8 + - - +
78G MET 3.2 1.0 + - - -
79G GLY* 2.8 26.4 + - - -
102G LEU* 3.4 31.8 + - + -
104G GLY* 4.9 0.2 - - - -
156G HIS* 2.9 49.7 + - - -
157G ILE* 4.0 17.9 - - + -
159G LEU* 4.3 3.1 - - + +
160G LEU* 3.8 40.9 - - + +
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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