Contacts of the strand formed by residues 162 - 167 (chain A) in PDB entry 1XSK
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 VAL 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 3.7 28.5 - - + -
161A THR* 1.3 76.7 - - - +
163A TYR* 1.3 69.0 + - - +
165A LEU* 5.2 0.4 - - + -
173A VAL* 3.5 7.3 - - - -
174A ARG* 2.8 38.8 + - + -
175A ASN* 2.8 18.4 + - - +
200A TYR* 3.6 33.7 - - + -
201A MET 3.5 2.2 - - - -
202A THR* 4.3 5.6 - - + -
220A VAL* 3.8 24.7 - - + -
228A VAL* 3.9 7.2 - - + -
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Residues in contact with TYR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A THR* 2.8 43.6 + - - -
162A VAL* 1.3 76.5 - - - +
164A GLY* 1.3 60.4 + - - +
172A LEU* 4.1 21.5 - - + +
173A VAL* 3.8 10.9 - - + +
174A ARG* 4.2 7.2 - - - +
200A TYR* 3.3 8.0 - - - +
201A MET* 2.9 44.6 + - + +
202A THR* 4.4 1.3 - - - -
203A ASN 4.1 2.7 - - - -
502A LEU* 3.7 34.1 - - + -
592A MET* 3.5 39.6 - - + +
602A ASP* 2.9 37.9 + - - -
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Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TYR* 1.3 77.2 - - - +
165A LEU* 1.3 72.2 + - - +
166A GLY 3.2 3.8 - - - +
172A LEU 5.0 0.6 + - - -
174A ARG* 2.8 35.1 + - - +
199A PHE 4.1 2.0 - - - -
499A SER* 4.2 9.3 + - - -
502A LEU* 4.3 11.6 - - - +
503A SER* 3.6 12.8 - - - -
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A VAL* 5.2 0.2 - - + -
164A GLY* 1.3 74.7 - - - +
166A GLY* 1.3 56.0 + - - +
168A ARG* 2.8 34.7 + - - -
174A ARG* 3.6 21.1 - - + -
179A VAL* 3.3 33.8 - - + +
181A THR* 4.8 2.3 - - + +
197A ILE 3.1 30.8 + - - +
199A PHE 2.8 26.2 + - - +
200A TYR* 4.1 12.3 - - + -
218A PHE* 3.7 41.5 - - + -
220A VAL* 4.1 10.1 - - + -
503A SER* 3.6 0.6 + - - -
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Residues in contact with GLY 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLY 3.7 1.9 - - - +
165A LEU* 1.3 80.6 - - - +
167A GLU* 1.3 61.5 + - - -
168A ARG* 3.1 9.6 + - - +
195A LYS 3.3 11.0 - - - -
197A ILE* 3.7 17.0 + - - -
499A SER* 3.4 19.1 - - - -
500A ILE* 4.3 4.9 - - - -
503A SER* 2.9 17.6 + - - -
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Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLY* 1.3 69.4 - - - -
168A ARG* 1.3 56.8 + - - +
169A PHE* 3.6 33.3 - - + -
193A ALA* 3.4 21.5 - - - +
194A TYR* 3.9 9.7 - - - +
195A LYS* 2.4 58.5 + - + +
480A GLY* 3.6 8.0 - - - -
496A GLY 3.8 20.2 - - - +
500A ILE* 3.9 16.6 - - + +
508A TRP* 3.1 27.0 + - - -
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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