Contacts of the helix formed by residues 141 - 144 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87F GLU 5.1 0.8 + - - +
88F LEU* 3.0 43.3 + - - +
89F GLY* 4.7 2.7 - - - +
136F LYS 3.4 5.9 + - - -
137F GLN* 3.6 22.5 + - - +
140F VAL* 1.3 74.8 - - - +
142F PRO* 1.3 67.5 - - + +
144F THR* 2.8 23.9 + - - +
145F SER* 5.0 0.9 + - - -
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Residues in contact with PRO 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F GLN 3.7 5.4 - - - +
138F ALA* 3.1 30.7 - - - +
140F VAL 3.4 4.7 - - - +
141F THR* 1.3 93.9 - - + +
143F PHE* 1.3 68.8 + - + +
144F THR 3.5 1.6 + - - -
145F SER* 4.5 7.8 + - - -
147F ASP* 5.2 0.9 - - - +
148F LYS* 3.6 25.4 + - + +
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Residues in contact with PHE 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F LEU* 5.1 0.3 - - - +
119F ASN* 3.1 25.4 + - - +
123F TYR* 3.7 24.2 - + + -
124F LEU* 3.8 7.7 - - + +
138F ALA 4.4 5.8 - - - -
139F TRP* 3.3 20.9 - + - -
140F VAL 2.9 11.2 + - - +
142F PRO* 1.3 96.6 - - + +
144F THR* 1.3 57.4 + - - +
145F SER 3.7 2.0 - - - -
146F GLY 5.2 0.4 + - - -
148F LYS* 3.5 17.8 - - + +
149F ILE 3.5 39.0 - - - -
150F GLY 3.9 2.0 - - - -
193F SER* 3.8 22.0 - - - -
194F ALA* 3.4 28.5 - - + -
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Residues in contact with THR 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F GLY* 3.8 12.0 - - - +
78F GLY* 5.1 3.1 - - - -
80F LEU* 4.7 5.2 - - - +
81F ALA* 3.7 29.7 + - + +
84F VAL* 4.4 1.6 - - + -
88F LEU 3.7 15.9 - - - +
89F GLY* 3.3 31.7 + - - +
90F GLY 4.4 0.7 - - - +
124F LEU* 4.5 1.8 - - + -
140F VAL* 3.3 29.2 - - + +
141F THR* 2.8 17.8 + - - +
142F PRO 3.5 0.4 - - - -
143F PHE* 1.3 78.4 - - - +
145F SER* 1.3 62.5 + - - +
146F GLY 3.7 1.7 + - - -
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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