Contacts of the strand formed by residues 162 - 165 (chain F) in PDB entry 1W4R
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 TYR 162 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F PRO* 3.5 7.2 - - - +
130F ARG* 3.3 43.1 - - + -
160F ALA 3.7 0.2 - - - -
161F ALA* 1.3 103.9 - - + +
163F THR* 1.3 63.8 + - - +
183F SER* 3.3 6.6 - - - -
184F VAL* 2.9 44.5 + - + +
185F CYS* 3.8 3.1 - - - -
186F ARG* 3.2 27.0 + - + -
189F TYR* 4.2 3.8 - - + -
141G PRO 3.3 26.2 - - - -
142G LEU 2.6 28.3 + - - -
143G ALA 4.0 2.0 - - - -
144G GLU* 2.9 26.9 + - + -
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Residues in contact with THR 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F PRO* 3.5 4.2 - - - +
28F MET* 3.0 47.7 + - + +
124F LEU* 4.3 1.9 - - - +
126F GLY 5.0 2.9 + - - -
127F THR 4.2 5.3 + - - +
128F PHE* 3.5 25.2 - - - +
130F ARG* 5.3 0.2 - - - +
162F TYR* 1.3 77.1 - - - +
164F LYS* 1.3 60.1 + - - +
181F TYR* 3.7 35.2 - - + -
182F HIS 3.5 7.4 - - - +
183F SER* 5.2 0.2 - - - -
184F VAL* 4.4 0.4 - - - -
189F TYR* 3.8 6.9 - - - -
300F TTP 3.8 14.7 - - + +
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Residues in contact with LYS 164 (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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128F PHE 4.9 0.2 - - - -
155F GLU* 2.8 37.0 + - - -
163F THR* 1.3 72.7 - - - +
165F ARG* 1.3 74.3 + - - +
166F LEU* 3.7 7.7 + - + +
181F TYR* 3.2 9.2 - - - +
182F HIS* 2.8 40.2 + - + +
184F VAL* 3.9 15.1 - - + +
188F CYS 2.7 25.5 + - - +
189F TYR* 3.9 27.5 + - + +
191F LYS* 4.5 22.0 - - + +
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Residues in contact with ARG 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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128F PHE* 3.3 50.6 + - + +
164F LYS* 1.3 84.9 - - - +
166F LEU* 1.3 65.4 + - - +
167F GLY 3.8 19.5 - - - +
169F GLU* 2.9 47.9 + - - +
171F GLU 2.8 20.6 + - - -
172F VAL 3.0 23.8 + - - -
174F VAL* 3.4 15.2 - - - +
180F LYS* 3.6 10.3 - - + +
181F TYR* 3.0 33.4 + - + -
300F TTP 3.7 1.4 + - - -
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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