Contacts of the helix formed by residues 164 - 174 (chain F) in PDB entry 6VVT
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 ASP 164 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D ARG* 5.2 2.7 - - - +
389D ARG* 4.1 14.6 + - - -
163F ALA* 1.3 82.3 + - + +
165F SER* 1.3 64.5 + - - +
166F VAL* 2.8 22.6 + - - +
167F ARG* 2.7 60.5 + - + +
168F ALA* 3.5 7.3 + - - +
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Residues in contact with SER 165 (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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130D TYR* 4.3 2.1 - - - +
372D ARG* 3.9 25.6 + - - +
376D GLU* 2.2 38.4 + - - -
387D ARG* 4.2 10.0 + - - +
164F ASP* 1.3 72.1 + - - +
166F VAL* 1.3 59.7 + - - +
167F ARG 3.0 1.6 - - - -
168F ALA* 2.7 30.1 + - - +
169F TYR* 3.2 11.0 + - - +
256F LEU* 4.8 9.6 - - - -
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Residues in contact with VAL 166 (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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389D ARG* 5.1 7.9 - - - +
164F ASP* 2.8 32.5 + - - +
165F SER* 1.3 74.9 - - - +
167F ARG* 1.3 61.8 + - - +
169F TYR* 3.6 3.1 + - + +
170F LEU* 3.1 35.5 + - + +
255F PHE* 4.2 29.6 - - + -
256F LEU* 4.2 30.1 - - + +
259F ILE* 5.1 1.3 - - + -
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Residues in contact with ARG 167 (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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163F ALA* 5.3 13.1 - - - +
164F ASP* 2.7 43.6 + - - +
166F VAL* 1.3 75.3 - - - +
168F ALA* 1.3 63.1 + - - +
170F LEU* 3.4 9.4 + - - +
171F LYS* 3.2 21.8 + - + +
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Residues in contact with ALA 168 (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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131D PHE 5.4 1.6 - - - +
132D ALA* 6.0 6.1 - - + -
372D ARG* 3.2 24.5 - - - +
164F ASP 3.5 5.9 + - - +
165F SER* 2.7 16.8 + - - +
167F ARG* 1.3 74.8 - - - +
169F TYR* 1.3 65.3 + - - +
171F LYS* 3.0 19.5 + - - +
172F GLN* 3.3 20.0 + - - +
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Residues in contact with TYR 169 (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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365D ILE* 4.4 17.7 - - + -
366D ILE* 4.9 0.4 - - - +
369D ASN* 3.2 44.2 - - + +
372D ARG* 3.8 15.3 - - - +
165F SER 3.2 6.3 + - - +
166F VAL* 4.0 10.3 - - + +
167F ARG 3.4 0.2 - - - -
168F ALA* 1.3 78.1 - - - +
170F LEU* 1.3 74.7 + - + +
172F GLN* 3.3 5.3 + - - +
173F ILE* 3.2 47.5 + - + +
238F LEU* 4.0 12.6 + - + +
242F VAL* 4.0 12.1 - - + -
256F LEU* 4.9 3.6 - - + -
259F ILE* 3.6 28.1 - - + +
260F GLN* 4.3 1.6 - - - -
263F ASN* 2.9 28.5 + - - -
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Residues in contact with LEU 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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166F VAL* 3.1 29.8 - - + +
167F ARG* 3.4 8.9 + - - +
168F ALA 3.1 0.8 - - - -
169F TYR* 1.3 93.3 - - + +
171F LYS* 1.3 64.5 + - - +
173F ILE* 3.4 18.7 - - + +
174F GLY* 3.0 22.9 + - - -
242F VAL* 4.3 20.0 - - + -
255F PHE* 5.9 2.9 - - + -
259F ILE* 5.2 2.0 - - + -
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Residues in contact with LYS 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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236D VAL* 5.5 5.3 + - - +
167F ARG* 3.2 14.1 + - + +
168F ALA* 3.0 13.9 + - - +
170F LEU* 1.3 76.1 - - - +
172F GLN* 1.3 63.0 + - + +
174F GLY* 4.1 1.5 - - - -
175F LYS* 3.9 12.8 + - - +
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Residues in contact with GLN 172 (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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131D PHE 4.6 11.2 + - - +
238D GLU* 5.0 14.1 + - + +
256D MET* 5.4 7.5 - - - +
365D ILE* 4.4 22.4 - - + +
372D ARG* 4.0 17.8 + - - -
168F ALA* 3.3 22.1 + - - +
169F TYR* 3.9 5.7 - - - +
170F LEU 3.1 0.6 - - - -
171F LYS* 1.3 81.6 - - + +
173F ILE* 1.3 67.1 + - - +
174F GLY 3.1 1.3 - - - -
175F LYS* 3.0 23.1 + - + +
176F VAL* 3.9 5.9 + - - +
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Residues in contact with ILE 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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365D ILE* 4.7 4.3 - - + -
169F TYR* 3.3 31.9 - - + +
170F LEU* 3.4 26.0 - - + +
172F GLN* 1.3 76.0 - - - +
174F GLY* 1.3 66.3 + - - +
175F LYS 3.2 1.0 + - - -
176F VAL* 3.2 25.9 + - - +
235F GLU 4.6 1.4 - - - +
236F ALA 5.8 0.2 - - - +
238F LEU* 3.5 35.6 - - + +
239F ARG* 4.3 30.0 + - + +
242F VAL* 3.7 30.1 - - + -
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Residues in contact with GLY 174 (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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170F LEU 3.0 17.5 + - - -
171F LYS* 4.4 3.6 - - - -
172F GLN 3.1 0.2 - - - -
173F ILE* 1.3 79.7 - - - +
175F LYS* 1.3 58.9 + - - +
176F VAL 3.4 2.9 - - - +
239F ARG* 3.2 32.9 + - - -
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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