Contacts of the strand formed by residues 113 - 117 (chain B) in PDB entry 2G73
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 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B HIS* 4.0 6.2 - - - -
26B THR 2.5 19.5 + - - +
27B ALA* 3.5 28.0 - - - +
29B THR* 2.3 39.4 + - - +
105B ARG* 3.5 35.4 - - - +
106B ALA 3.5 8.5 - - - +
107B THR* 3.7 19.3 - - + +
111B GLY 4.1 3.6 - - - +
112B ILE* 1.3 78.8 - - - +
114B GLU* 1.3 78.9 + - - +
115B ASN* 4.3 0.7 - - + +
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Residues in contact with GLU 114 (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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25B HIS* 2.9 16.1 + - + -
32B HIS* 2.9 10.7 + - - -
57B ALA* 4.8 7.9 - - + -
58B TRP* 3.9 19.4 - - + -
69B HIS* 3.4 5.2 + - - -
104B PHE* 3.7 24.2 - - + -
105B ARG* 3.3 2.1 - - - -
106B ALA 2.8 35.5 + - - +
112B ILE 3.9 1.2 + - - -
113B VAL* 1.3 77.9 - - - +
115B ASN* 1.3 56.0 + - - +
116B GLU* 2.6 17.4 - - - +
184B MN 2.2 36.9 + - - -
186B EIP 3.5 24.3 + - - +
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Residues in contact with ASN 115 (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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29B THR* 3.5 29.2 + - + +
30B ARG* 4.4 0.6 - - - +
31B LEU* 3.3 25.8 - - - +
32B HIS* 3.1 28.9 + - - -
103B ARG* 2.5 33.6 + - - +
104B PHE 3.5 2.2 - - - -
105B ARG* 3.6 24.4 - - - +
113B VAL* 4.5 0.2 - - + -
114B GLU* 1.3 77.1 + - - +
116B GLU* 1.3 60.5 + - - +
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Residues in contact with GLU 116 (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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31B LEU* 4.0 4.3 - - - -
32B HIS* 3.1 13.1 + - - +
34B ALA* 3.3 19.0 - - + +
103B ARG* 3.4 7.1 - - - +
104B PHE* 2.8 55.3 + - + -
114B GLU* 3.0 12.2 - - - +
115B ASN* 1.3 79.8 + - - +
117B VAL* 1.3 65.2 + - - +
118B CYS* 3.8 3.8 + - + +
184B MN 2.4 30.8 + - - -
186B EIP 1.6 52.0 - - - +
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Residues in contact with VAL 117 (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 LEU* 3.3 34.8 - - + -
13B GLY* 4.5 9.9 - - - -
31B LEU* 4.3 17.3 - - + -
32B HIS 3.0 5.4 + - - +
33B LEU* 3.5 12.1 - - + +
34B ALA 2.8 30.2 + - - +
101B ASP* 6.4 0.4 - - - -
102B PHE 4.1 6.7 - - - +
103B ARG* 4.3 12.3 - - + -
116B GLU* 1.3 73.5 - - - +
118B CYS* 1.3 59.9 + - - +
119B PRO* 3.6 6.5 - - + -
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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