Contacts of the helix formed by residues 137 - 140 (chain A) in PDB entry 2V3V
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 PRO 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A SER* 4.3 0.4 - - - -
110A GLY 3.7 16.2 - - - +
135A GLY* 3.2 9.2 - - - +
136A ASN* 1.4 100.6 - - - +
138A ARG* 1.3 52.8 + - - +
140A CYS* 2.9 11.7 + - + -
141A MET* 2.7 25.2 + - + -
142A ALA 3.4 0.2 + - - -
346A GLN* 3.8 7.2 - - - +
349A ALA* 3.9 19.1 - - + -
353A VAL* 3.7 25.1 - - + -
814A LCP 2.7 34.9 + - + +
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Residues in contact with ARG 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASP* 2.8 38.4 + - - +
135A GLY 3.1 18.1 + - - +
137A PRO* 1.3 75.3 - - - +
139A LEU* 1.3 58.2 + - + +
140A CYS 3.2 1.1 + - - -
142A ALA* 3.6 5.8 - - - +
359A LEU* 4.0 10.3 - - + +
360A SER* 3.5 8.1 + - - -
361A HIS* 3.2 33.2 + - - -
396A HIS* 3.4 22.6 - - - +
397A THR* 3.5 26.5 - - - +
398A VAL* 5.3 0.4 - - + +
707A VAL 5.0 0.2 + - - -
708A SER 3.0 26.8 + - - -
709A ARG* 3.7 15.8 - - - +
710A GLU* 3.3 27.0 - - - +
711A PRO* 3.9 0.2 - - - +
814A LCP 2.9 11.3 + - - -
815A LCP 3.5 13.5 + - - -
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TYR* 3.6 20.2 - - - +
136A ASN* 2.7 25.8 + - + +
138A ARG* 1.3 77.1 - - + +
140A CYS* 1.3 58.9 + - - +
312A GLN* 3.3 22.5 + - - +
397A THR* 3.9 14.4 - - + -
398A VAL* 5.2 1.6 - - + -
422A THR* 4.3 7.6 - - - +
423A LEU* 3.9 21.5 - - + -
424A PRO* 4.7 0.7 - - + -
710A GLU* 3.5 9.0 - - - +
711A PRO* 3.8 23.6 - - + -
713A TYR* 3.4 34.3 - - + +
811A MGD 3.8 19.5 - - + -
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Residues in contact with CYS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASN 4.0 7.2 - - - +
137A PRO* 2.9 7.2 + - + +
138A ARG 3.2 1.8 - - - -
139A LEU* 1.3 81.3 - - - +
141A MET* 1.3 66.0 + - - +
308A MET* 3.4 14.7 - - - +
311A ASN* 3.3 15.4 + - - +
345A GLY 4.4 0.2 - - - -
710A GLU* 2.4 25.6 + - - +
810A MO 2.4 31.9 - - - +
811A MGD 3.2 4.7 - - + -
812A MGD 3.1 17.0 - - - -
813A UNX 2.4 17.9 - - - -
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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