Contacts of the strand formed by residues 162 - 165 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141E PRO 3.3 24.2 - - - -
142E LEU 2.6 26.8 + - - -
143E ALA 3.6 4.1 - - - -
144E GLU* 3.0 25.5 + - + -
27H PRO* 3.5 6.7 - - - +
130H ARG* 3.4 39.5 - - + -
160H ALA 3.6 0.2 - - - -
161H ALA* 1.3 101.8 - - + +
163H THR* 1.3 64.4 + - - +
183H SER* 3.4 6.8 - - - -
184H VAL* 2.9 37.0 + - + +
185H CYS* 3.8 3.6 - - - -
186H ARG* 3.3 37.0 + - + -
189H TYR* 4.2 11.2 - - + -
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Residues in contact with THR 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H PRO* 3.6 4.7 - - - +
28H MET* 2.9 49.2 + - + +
124H LEU* 4.3 1.7 - - - +
126H GLY 5.0 3.3 + - - -
127H THR 4.1 5.2 + - - +
128H PHE* 3.4 25.6 - - - +
130H ARG* 5.4 0.6 - - - +
162H TYR* 1.3 76.0 - - - +
164H LYS* 1.3 60.3 + - - +
181H TYR* 3.6 33.0 - - + -
182H HIS 3.5 7.0 - - - +
183H SER* 5.3 0.2 - - - -
184H VAL* 4.5 0.4 - - - -
189H TYR* 3.8 7.2 - - - -
300H TTP 3.7 15.2 - - + +
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Residues in contact with LYS 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H PHE 4.8 0.2 - - - -
155H GLU* 2.9 36.8 + - - -
163H THR* 1.3 71.9 - - - +
165H ARG* 1.3 72.8 + - - +
166H LEU* 3.7 10.5 + - + -
181H TYR* 3.2 9.3 - - - +
182H HIS* 2.8 37.8 + - + +
184H VAL* 3.8 15.4 - - + +
188H CYS 2.7 29.5 + - - +
189H TYR* 4.2 23.5 + - + +
191H LYS* 4.5 10.7 - - - +
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Residues in contact with ARG 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H PHE* 3.3 52.7 + - + +
164H LYS* 1.3 82.3 - - - +
166H LEU* 1.3 64.6 + - - +
167H GLY* 3.7 19.7 - - - +
169H GLU* 3.0 46.1 + - - +
171H GLU 2.7 20.2 + - - -
172H VAL 2.9 27.1 + - - -
174H VAL* 3.5 15.5 - - - +
180H LYS* 3.7 9.4 - - + +
181H TYR* 3.0 31.1 + - + -
300H 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