Contacts of the strand formed by residues 162 - 166 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU* 3.6 30.7 - - + -
161D THR* 1.3 76.1 - - - +
163D TYR* 1.3 68.2 + - - +
165D LEU* 5.5 0.4 - - + -
173D VAL* 3.5 7.8 - - - +
174D ARG* 3.0 31.5 + - + -
175D ASN* 2.8 18.3 + - - +
200D TYR* 3.6 36.6 - - + -
201D MET 3.6 2.7 - - - +
202D THR* 4.1 4.5 - - + -
220D VAL* 3.8 31.9 - - + -
228D VAL* 3.9 4.3 - - + -
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Residues in contact with TYR 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D THR* 2.8 42.2 + - - -
162D VAL* 1.3 76.7 - - - +
164D GLY* 1.3 62.3 + - - +
172D LEU* 4.1 21.8 - - + +
173D VAL* 3.8 11.0 - - + -
174D ARG* 4.0 7.6 - - - -
200D TYR* 3.3 9.9 - - - +
201D MET* 2.9 44.2 + - + +
202D THR* 4.4 1.6 - - - -
203D ASN 4.2 2.0 - - - -
502D LEU* 3.8 32.8 - - + -
592D MET* 3.4 40.3 - - + +
602D ASP* 2.7 38.8 + - - -
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Residues in contact with GLY 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D TYR* 1.3 77.6 - - - +
165D LEU* 1.3 73.4 + - - +
166D GLY 3.3 4.4 + - - +
168D ARG* 4.1 0.2 - - - -
172D LEU 5.0 0.4 + - - -
174D ARG* 2.9 32.7 + - - +
199D PHE 4.1 1.6 - - - -
200D TYR* 4.8 0.2 - - - -
499D SER* 4.2 7.7 + - - -
502D LEU* 4.0 15.6 - - - +
503D SER* 3.5 13.2 - - - -
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D VAL* 5.5 0.7 - - + -
164D GLY* 1.3 74.8 - - - +
166D GLY* 1.3 53.4 + - - +
168D ARG* 2.7 40.3 + - - -
174D ARG* 4.0 15.0 - - + -
179D VAL* 3.6 33.7 - - + -
181D THR* 4.8 2.4 - - + +
197D ILE 3.0 32.3 + - - +
199D PHE 2.8 28.6 + - - +
200D TYR* 4.0 11.2 - - + -
218D PHE* 3.8 39.5 - - + -
220D VAL* 4.1 16.6 - - + -
503D SER* 3.5 1.2 + - - -
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Residues in contact with GLY 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D GLY 3.8 1.7 - - - +
165D LEU* 1.3 79.1 - - - +
167D GLU* 1.3 61.7 + - - -
168D ARG* 3.1 10.7 + - - +
195D LYS* 3.4 11.7 - - - -
197D ILE* 3.7 18.6 + - - +
499D SER* 3.3 21.8 - - - +
500D ILE* 4.4 2.5 - - - -
503D SER* 3.0 15.5 + - - -
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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