Contacts of the strand formed by residues 162 - 165 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B PRO 3.3 21.1 - - - -
142B LEU 2.7 27.2 + - - -
143B ALA 4.1 2.2 - - - -
144B GLU* 2.9 26.8 + - + -
27C PRO* 3.5 7.6 - - - +
130C ARG* 3.1 39.7 - - + -
161C ALA* 1.3 102.6 - - + +
163C THR* 1.3 63.9 + - - +
183C SER* 3.3 6.8 - - - -
184C VAL* 2.8 38.7 + - + +
185C CYS* 3.8 3.6 - - - -
186C ARG* 3.2 35.2 + - + -
189C TYR* 4.1 13.7 - - + -
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Residues in contact with THR 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C PRO* 3.6 4.4 - - - +
28C MET* 3.0 50.3 + - + +
124C LEU* 4.3 1.9 - - - +
126C GLY 5.1 2.8 + - - -
127C THR 4.1 4.3 + - - +
128C PHE* 3.4 25.4 - - - +
130C ARG* 5.4 0.4 - - - +
162C TYR* 1.3 75.8 - - - +
164C LYS* 1.3 61.8 + - - +
181C TYR* 3.6 33.0 - - + -
182C HIS 3.5 7.0 - - - +
184C VAL* 4.5 0.2 - - - -
189C TYR* 3.7 7.6 - - - -
300C TTP 3.7 15.0 - - + +
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Residues in contact with LYS 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C PHE 4.8 0.7 - - - -
155C GLU* 2.8 38.3 + - - -
163C THR* 1.3 74.0 - - - +
165C ARG* 1.3 73.1 + - - +
166C LEU* 3.8 6.9 + - + +
181C TYR* 3.2 8.7 - - - +
182C HIS* 2.9 35.1 + - + +
184C VAL* 3.8 18.1 - - + +
188C CYS 2.7 24.9 + - - +
189C TYR* 3.8 27.9 + - + +
191C LYS* 4.7 12.1 + - - +
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Residues in contact with ARG 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C PHE* 3.2 49.3 + - + +
164C LYS* 1.3 83.6 - - - +
166C LEU* 1.3 64.4 + - - +
167C GLY 3.7 19.3 - - - +
169C GLU* 2.9 43.8 + - - +
171C GLU 2.7 21.8 + - - -
172C VAL 2.9 24.0 + - - -
174C VAL* 3.4 17.0 - - - +
180C LYS* 3.7 9.6 - - + +
181C TYR* 2.9 34.1 + - + -
300C TTP 3.6 3.6 + - - -
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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