Contacts of the strand formed by residues 141 - 145 (chain V) in PDB entry 5GJQ
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 141 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29V GLU* 5.9 1.1 - - - +
31V VAL* 5.0 12.8 - - + -
57V MET* 5.0 4.0 - - + -
67V VAL* 4.6 19.1 - - + -
69V VAL* 5.7 2.7 - - + -
109V VAL 3.2 13.5 + - - +
110V GLY* 3.2 25.6 - - - -
111V TRP* 3.3 10.9 + - - -
130V GLN* 3.5 7.4 - - - +
139V ARG* 3.5 16.6 - - - +
140V ALA* 1.3 73.6 - - - +
142V ALA* 1.3 60.4 + - - +
143V VAL* 4.4 17.3 - - + -
159V ALA* 5.2 2.0 - - + -
160V PHE 4.2 7.9 - - - +
161V ARG* 4.2 6.1 - - - -
203V ILE* 4.0 25.6 - - + -
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Residues in contact with ALA 142 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111V TRP* 3.7 15.9 - - + +
113V HIS* 6.5 0.2 - - + -
122V LEU* 4.2 28.0 - - + -
130V GLN* 3.1 19.7 + - - +
141V VAL* 1.3 72.6 - - - +
143V VAL* 1.3 62.3 + - - +
144V VAL* 4.1 1.2 + - - -
158V ASP 3.9 0.3 - - - +
159V ALA* 3.0 3.3 - - - +
160V PHE* 2.8 49.5 + - + +
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Residues in contact with VAL 143 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31V VAL* 6.1 0.7 - - + -
33V ILE* 5.2 7.9 - - + -
41V MET* 4.5 7.9 - - + -
57V MET* 3.5 36.3 - - + -
111V TRP* 3.1 8.4 + - - +
112V TYR* 3.2 26.4 - - + -
113V HIS* 3.3 11.8 + - - +
141V VAL* 4.4 7.2 - - + -
142V ALA* 1.3 76.3 - - - +
144V VAL* 1.3 62.7 + - - +
145V VAL* 4.2 7.6 - - + -
157V ILE* 4.0 23.3 - - + -
158V ASP 3.3 9.4 - - - +
159V ALA* 3.6 19.5 - - + -
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Residues in contact with VAL 144 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113V HIS* 3.8 16.8 - - + -
114V SER* 4.9 0.7 - - - -
115V HIS* 4.3 12.3 - - + +
119V GLY 4.1 5.8 - - - +
120V CYS* 3.7 37.6 - - + -
121V TRP 3.9 9.2 - - - +
122V LEU* 3.7 29.8 - - + -
142V ALA* 5.4 0.4 - - + -
143V VAL* 1.3 75.6 - - - +
145V VAL* 1.3 71.8 + - - +
157V ILE* 3.7 1.9 - - - +
158V ASP* 2.7 38.2 + - + +
160V PHE* 4.5 9.4 - - + -
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Residues in contact with VAL 145 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41V MET* 3.4 32.3 - - + +
42V LEU* 3.6 33.4 - - + -
45V GLY* 6.0 2.5 - - - -
112V TYR* 4.8 0.7 - - + -
113V HIS 3.2 18.3 + - - +
114V SER* 2.9 28.3 - - - -
115V HIS 3.0 6.2 + - - -
120V CYS* 4.7 0.2 - - - -
143V VAL* 4.2 5.4 - - + -
144V VAL* 1.3 77.8 - - - +
146V ASP* 1.3 67.0 + - - +
147V PRO* 3.9 5.8 - - + -
156V VAL 4.3 4.5 - - - +
157V ILE* 3.4 27.6 - - + -
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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
------------------------------------------------------------
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