Contacts of the strand formed by residues 166 - 170 (chain F) in PDB entry 1II4
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 LEU 166 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B TYR* 2.6 38.7 + - + -
38B GLY* 4.5 3.1 - - - +
40B PHE* 3.5 37.5 - - + -
53B ARG* 5.3 7.6 - - + +
55B LYS* 5.5 4.5 - - + -
151B MET* 5.2 3.8 - - + -
164F LYS* 3.7 10.1 - - - +
165F ARG* 1.3 78.3 - - + +
167F HIS* 1.3 60.4 + - - +
168F ALA* 4.5 4.0 - - + +
245F HIS* 3.5 30.3 - - + +
247F ASP* 4.5 15.0 - - + +
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Residues in contact with HIS 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 3.5 2.9 - - - -
164F LYS* 3.1 59.3 + - + +
165F ARG 4.0 2.6 + - - -
166F LEU* 1.3 73.4 - - - +
168F ALA* 1.3 60.4 + - - +
169F VAL* 4.0 9.2 - - + -
175F VAL* 4.6 9.6 - - + -
176F LYS 4.6 8.2 + - - -
177F PHE* 3.5 36.3 - + + -
244F TYR* 4.0 14.1 - + - -
245F HIS 2.8 10.3 + - - +
246F LEU* 3.4 11.4 - - + +
247F ASP 2.9 23.7 + - - -
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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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33B TYR* 3.3 38.4 + - + -
112B TYR* 4.2 4.3 + - - -
149B LEU* 3.4 11.0 - - + +
151B MET* 3.5 41.3 - - + -
164F LYS* 5.8 0.4 + - - +
166F LEU* 3.9 3.1 - - + -
167F HIS* 1.3 73.6 - - - +
169F VAL* 1.3 64.9 + - - +
247F ASP* 3.2 9.4 - - + +
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Residues in contact with VAL 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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112B TYR* 3.9 10.1 - - - +
149B LEU* 3.6 6.5 - - - +
164F LYS* 5.9 3.4 - - - +
167F HIS* 4.6 13.2 - - + -
168F ALA* 1.3 83.7 - - - +
170F PRO* 1.3 75.3 - - + +
173F ASN* 4.5 7.4 - - + -
174F THR 5.6 2.2 - - - +
175F VAL* 3.7 31.9 - - + -
221F VAL* 3.7 19.1 - - + -
246F LEU* 4.4 7.2 - - + -
247F ASP 3.0 8.0 + - - +
248F VAL* 3.4 3.5 - - + -
249F VAL 3.0 19.9 + - - -
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Residues in contact with PRO 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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110B ASN 3.8 12.6 - - - +
111B ASN* 3.5 30.5 - - + +
112B TYR* 3.4 26.2 - - + +
149B LEU* 3.8 8.6 - - + -
169F VAL* 1.3 91.3 - - + +
171F ALA* 1.3 70.3 + - - +
173F ASN* 3.3 36.4 + - - +
249F VAL 3.1 10.8 - - - +
251F ARG* 4.3 3.1 - - + -
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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