Contacts of the helix formed by residues 141 - 144 (chain C) in PDB entry 2VIG
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 141 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C GLU 5.9 0.2 - - - +
88C LEU* 2.9 48.1 + - - +
89C GLY* 5.1 2.5 - - - -
136C LYS 3.3 3.3 + - - -
137C GLN* 3.5 12.9 + - - +
140C VAL* 1.3 77.3 - - - +
142C PRO* 1.3 65.6 - - + +
144C THR* 2.7 22.9 + - - +
145C SER* 5.3 1.4 + - - -
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Residues in contact with PRO 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C GLN 3.5 6.3 - - - +
138C ALA* 3.3 27.6 - - - +
139C TRP 4.2 1.1 - - - -
140C VAL 3.4 5.2 - - - +
141C THR* 1.3 95.2 - - + +
143C PHE* 1.3 66.1 + - + +
144C THR 3.5 1.3 + - - -
145C SER* 4.7 4.1 + - - +
147C ASP* 4.7 5.9 - - - +
148C LYS* 3.6 34.7 + - + +
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Residues in contact with PHE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C LEU* 5.1 0.5 - - - +
119C ASN* 3.1 25.3 + - - +
123C TYR* 3.6 26.5 - + + -
124C LEU* 3.9 6.0 - - + +
138C ALA 4.5 3.4 - - - -
139C TRP* 3.3 25.8 - + - -
140C VAL 2.6 17.0 + - - +
142C PRO* 1.3 82.6 - - + +
144C THR* 1.3 57.2 + - - +
145C SER 3.6 2.2 - - - -
146C GLY 5.1 0.3 + - - -
148C LYS* 3.3 31.8 - - + +
149C ILE 3.2 37.2 - - - -
193C SER* 3.6 22.2 - - - -
194C ALA* 3.4 30.5 - - + -
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Residues in contact with THR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C GLY 3.7 8.7 - - - +
78C GLY* 5.1 2.6 - - - -
80C LEU* 4.5 5.5 - - - +
81C ALA* 3.7 35.8 + - + +
84C VAL* 4.2 3.8 - - + -
88C LEU 4.0 15.9 - - - +
89C GLY* 3.5 27.3 + - - +
124C LEU* 4.5 2.5 - - + -
140C VAL* 3.5 27.4 - - + +
141C THR* 2.7 19.8 + - - +
142C PRO 3.5 1.4 - - - -
143C PHE* 1.3 79.4 - - - +
145C SER* 1.3 63.5 + - - +
146C GLY 3.7 1.3 - - - -
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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