Contacts of the strand formed by residues 162 - 166 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E LEU* 3.9 27.8 - - + -
161E THR* 1.3 76.7 - - - +
163E TYR* 1.3 66.1 + - - +
165E LEU* 5.2 0.2 - - + -
173E VAL* 3.5 6.2 - - - -
174E ARG* 2.7 45.8 + - + -
175E ASN* 3.0 10.9 + - - +
200E TYR* 3.8 31.4 - - + -
201E MET 3.6 2.7 - - - -
202E THR* 4.2 4.5 - - + -
220E VAL* 3.6 31.9 - - + -
228E VAL* 3.9 7.2 - - + -
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Residues in contact with TYR 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E THR* 2.8 41.1 + - - -
162E VAL* 1.3 77.4 - - - +
164E GLY* 1.3 60.8 + - - +
172E LEU* 4.1 21.8 - - + +
173E VAL* 3.7 11.8 - - + +
174E ARG* 4.2 7.0 - - - +
200E TYR* 3.3 6.4 - - - +
201E MET* 2.8 47.0 + - + +
202E THR* 4.4 1.6 - - - -
203E ASN* 4.2 2.9 - - - +
502E LEU* 3.8 35.7 - - + -
592E MET* 3.8 37.4 - - + +
602E ASP* 2.7 40.4 + - - +
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Residues in contact with GLY 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E TYR* 1.3 76.3 - - - +
165E LEU* 1.3 74.0 + - - +
166E GLY 3.2 4.2 + - - +
172E LEU 5.1 0.2 + - - -
174E ARG* 2.7 35.0 + - - +
199E PHE 4.1 2.7 - - - -
200E TYR* 4.7 0.2 - - - -
499E SER* 4.4 6.4 + - - -
502E LEU* 4.4 12.6 - - - +
503E SER* 3.6 14.1 - - - -
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Residues in contact with LEU 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E VAL* 5.2 0.4 - - + -
164E GLY* 1.3 74.6 - - - +
166E GLY* 1.3 58.5 + - - +
168E ARG* 3.0 31.9 + - - -
174E ARG* 3.8 21.1 - - + -
179E VAL* 3.1 35.4 - - + +
181E THR* 4.9 1.6 - - + +
197E ILE 3.0 26.1 + - - +
199E PHE 2.7 29.6 + - - +
200E TYR* 3.8 19.1 - - + -
218E PHE* 3.9 31.6 - - + -
220E VAL* 4.1 9.9 - - + -
503E SER* 3.7 0.6 + - - -
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Residues in contact with GLY 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E GLY 3.7 1.9 - - - +
165E LEU* 1.3 80.5 - - - +
167E GLU* 1.3 61.7 + - - -
168E ARG* 3.1 10.0 + - - +
195E LYS 3.6 10.1 - - - -
197E ILE* 3.8 18.9 + - - +
499E SER* 3.3 19.2 - - - -
500E ILE* 5.7 0.4 - - - -
503E SER* 3.0 22.0 + - - -
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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