Contacts of the helix formed by residues 169 - 177 (chain F) in PDB entry 3VBB
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 SER 169 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167F LYS 4.3 0.8 + - - -
168F TYR* 1.3 75.2 - - - +
170F HIS* 1.3 67.5 + - - +
171F VAL* 3.7 27.5 + - - +
172F ASP* 3.3 13.1 + - - -
173F LEU* 3.0 24.7 + - - +
385F GLY 4.5 5.3 + - - -
386F SER* 3.5 17.3 + - - -
442F GLU* 3.7 5.8 - - - -
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Residues in contact with HIS 170 (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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169F SER* 1.3 74.3 + - - +
171F VAL* 1.3 81.9 + - + +
173F LEU* 4.0 7.6 - - - -
174F VAL* 2.8 35.4 + - + +
315F ILE 4.8 3.6 + - - -
316F PHE* 3.5 35.1 + + + +
383F PHE* 4.6 6.5 - + - -
386F SER* 3.7 8.9 + - - -
390F ARG* 4.4 5.4 + - - -
438F CYS* 3.5 37.1 - - + +
441F LEU* 5.2 2.2 - - + -
442F GLU* 3.0 41.8 + - + +
601F PO4 3.4 21.9 + - - -
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Residues in contact with VAL 171 (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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169F SER* 3.7 19.1 - - - +
170F HIS* 1.3 102.6 - - + +
172F ASP* 1.3 79.1 + - - +
174F VAL* 3.9 6.7 + - - +
175F VAL* 3.7 18.5 + - - +
180F PHE* 5.5 1.6 - - - -
312F THR* 5.5 5.6 - - - -
313F ARG 4.7 16.0 - - - +
314F GLY* 4.5 15.7 - - - +
475F PRO* 5.2 0.7 - - - +
601F PO4 4.6 11.7 - - - +
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Residues in contact with ASP 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F TYR* 4.3 12.2 - - + -
169F SER* 3.3 25.1 + - - +
171F VAL* 1.3 87.8 - - - +
173F LEU* 1.3 61.5 + - - +
174F VAL 3.1 0.4 - - - -
175F VAL* 3.1 5.0 + - - +
176F MET* 2.8 42.9 + - - +
474F ALA* 4.3 4.0 - - + -
475F PRO* 4.1 36.0 - - + +
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Residues in contact with LEU 173 (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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168F TYR* 3.5 28.9 - - + +
169F SER 3.0 27.2 + - - +
170F HIS* 3.3 8.3 + - - +
172F ASP* 1.3 77.6 - - - +
174F VAL* 1.3 61.9 + - - +
176F MET* 3.9 6.2 - - - -
177F VAL* 3.1 30.0 + - - +
441F LEU* 4.0 24.6 - - + +
442F GLU* 4.2 4.0 - - - -
445F GLN* 3.6 23.3 - - + +
450F ILE* 3.6 16.6 - - + -
470F PHE* 3.5 33.4 - - + -
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Residues in contact with VAL 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F HIS* 2.8 30.0 + - + +
171F VAL* 4.1 6.3 - - - +
172F ASP 3.1 0.2 - - - -
173F LEU* 1.3 77.5 - - - +
175F VAL* 1.3 59.1 - - - +
177F VAL* 3.9 1.6 + - - +
178F ASP 3.8 0.9 + - - -
179F GLY* 3.1 24.4 + - - -
180F PHE* 3.0 36.4 - - + +
200F LEU* 3.7 21.1 - - + -
314F GLY* 6.1 1.1 - - - -
315F ILE* 4.1 27.6 - - + +
438F CYS* 5.0 1.1 - - - -
441F LEU* 3.9 19.5 - - + -
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Residues in contact with VAL 175 (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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171F VAL 3.7 14.8 - - - +
172F ASP 3.1 6.3 + - - +
174F VAL* 1.3 73.3 - - - +
176F MET* 1.3 54.6 + - - +
177F VAL 2.9 4.7 - - - -
178F ASP* 2.6 29.6 + - - +
180F PHE* 4.1 26.2 - - + +
313F ARG* 6.2 1.1 - - - +
472F LYS* 3.7 30.3 - - + +
473F PRO 4.8 3.1 - - - +
475F PRO* 3.9 28.5 - - + -
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Residues in contact with MET 176 (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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168F TYR* 3.9 29.8 - - + +
172F ASP 2.8 29.8 + - - +
173F LEU* 4.0 4.0 - - - +
175F VAL* 1.3 71.7 - - - +
177F VAL* 1.3 58.2 + - - +
178F ASP 3.3 0.2 - - - -
470F PHE* 3.3 51.0 - - + -
471F VAL 2.7 26.5 + - - -
472F LYS* 3.1 28.0 + - - +
473F PRO 3.9 0.9 - - - +
474F ALA* 3.3 41.5 - - + +
475F PRO* 4.4 0.2 - - + -
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Residues in contact with VAL 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F LEU 3.1 13.5 + - - +
174F VAL 4.4 0.7 - - - +
175F VAL 2.8 1.8 + - - -
176F MET* 1.3 79.2 - - - +
178F ASP* 1.3 64.9 + - - +
179F GLY 4.0 7.2 - - - +
199F VAL* 3.2 33.4 - - + +
200F LEU* 4.1 17.0 - - + -
441F LEU* 5.4 0.9 - - + -
450F ILE* 3.6 26.9 - - + -
468F ILE* 3.4 26.5 - - + +
469F PRO 4.1 15.9 - - - +
470F PHE* 4.2 6.3 - - + -
471F VAL* 4.5 6.6 - - - +
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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
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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