Contacts of the strand formed by residues 109 - 115 (chain B) in PDB entry 6G1V
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 THR 109 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PRO* 3.6 23.3 - - + -
108B SER* 1.3 74.1 - - - +
110B THR* 1.3 79.8 + - - +
111B VAL 3.5 0.2 + - - -
140B GLU 3.2 20.2 + - - +
141B VAL 4.3 0.2 - - - -
142B VAL* 3.6 22.9 - - + +
188B GLY 2.9 18.7 + - - +
189B GLY* 3.4 1.9 - - - -
190B ASP* 2.7 30.6 + - - +
478B LYS* 5.1 3.1 - - - -
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Residues in contact with THR 110 (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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109B THR* 1.3 78.5 + - - +
111B VAL* 1.3 68.0 + - - +
141B VAL* 3.5 16.4 - - + +
142B VAL 3.0 24.1 + - - -
193B THR* 3.7 20.9 - - - +
195B THR* 5.1 0.2 - - - +
477B ALA* 3.6 40.4 - - + +
478B LYS* 2.9 36.5 + - + +
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Residues in contact with VAL 111 (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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109B THR 3.6 11.0 - - - +
110B THR* 1.3 79.1 - - - +
112B MET* 1.3 61.8 + - - +
113B VAL* 4.0 22.4 - - + -
142B VAL* 3.3 13.0 - - + +
144B VAL* 4.2 13.5 - - + -
180B VAL* 4.3 1.6 - - + -
184B ILE* 3.9 17.0 - - + -
189B GLY* 3.7 20.2 - - - -
190B ASP 3.7 12.3 - - - +
193B THR 3.0 6.2 + - - +
194B VAL* 3.3 17.5 - - + -
195B THR* 2.7 31.7 + - - -
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Residues in contact with MET 112 (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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110B THR* 4.6 1.8 - - + -
111B VAL* 1.3 79.2 - - - +
113B VAL* 1.3 61.9 + - - +
135B LEU* 4.5 12.1 - - + -
141B VAL* 4.2 21.3 - - + -
142B VAL 3.0 7.0 + - - +
143B LEU* 3.3 12.4 - - + +
144B VAL* 2.8 26.7 + - - +
195B THR* 3.2 7.4 - - + +
197B PHE* 3.7 31.6 - - + -
223B ILE* 4.2 13.5 - - + -
473B TRP* 3.9 31.6 - - + +
474B ALA* 4.1 14.4 - - - -
477B ALA* 3.8 21.3 - - + -
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Residues in contact with VAL 113 (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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111B VAL* 4.0 7.2 - - + -
112B MET* 1.3 74.7 - - - +
114B TRP* 1.3 62.2 + - - +
115B ILE* 4.2 2.2 - - + +
144B VAL* 3.2 28.7 - - + +
146B LEU* 3.6 33.7 - - + -
177B LEU* 4.0 14.6 - - + -
180B VAL* 4.3 13.9 - - + -
194B VAL* 3.6 24.2 - - + -
195B THR 2.7 11.2 + - - +
196B ILE* 3.4 6.2 - - + +
197B PHE* 2.9 29.4 + - - +
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Residues in contact with TRP 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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113B VAL* 1.3 71.1 - - - +
115B ILE* 1.3 66.3 + - - +
116B TYR* 3.8 14.1 + + + +
117B GLY 5.1 0.4 - - - -
125B SER* 5.6 0.2 - - - -
130B TYR* 3.4 59.2 - + + -
143B LEU* 5.0 1.3 - - + -
144B VAL 2.7 16.1 + - - +
145B SER* 3.7 15.6 - - - -
146B LEU* 3.2 28.8 + - - +
197B PHE* 3.3 60.6 - + + -
198B GLY* 3.6 14.6 - - - -
199B GLU* 3.6 33.7 - - + -
225B GLN* 3.9 13.2 - - - -
444B ILE* 4.3 4.7 - - + -
448B PHE* 3.5 24.5 - + + -
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Residues in contact with ILE 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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113B VAL* 4.2 5.4 - - + +
114B TRP* 1.3 79.4 - - - +
116B TYR* 1.3 64.7 + - - +
117B GLY 3.7 0.5 + - - -
146B LEU* 3.9 25.8 - - + -
148B TYR* 3.8 9.9 - - + -
173B GLN* 3.8 39.9 - - + +
177B LEU* 5.3 1.3 - - + -
196B ILE* 4.6 11.9 - - + -
197B PHE 2.8 15.4 + - - +
198B GLY* 3.2 19.2 - - - -
199B GLU 3.7 1.2 + - - -
202B GLY* 3.3 19.9 - - - +
205B SER* 4.1 2.2 - - - -
206B VAL* 4.1 19.1 - - + -
209B HIS* 4.3 13.2 - - + +
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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