Contacts of the strand formed by residues 262 - 265 (chain A) in PDB entry 1XGS
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 ILE 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A TYR* 3.7 20.2 - - + -
207A MET 3.2 11.2 - - - +
208A TYR* 4.0 13.5 - - + -
209A VAL* 4.1 4.3 - - - +
223A LEU* 4.4 7.2 - - + -
226A ILE* 4.3 10.8 - - + -
235A PHE* 4.1 13.9 - - + -
253A LEU* 3.7 42.0 - - + +
256A LEU* 3.6 9.6 + - + -
257A GLU* 3.7 36.2 - - + +
260A GLY* 4.3 2.6 - - - -
261A ALA* 1.3 88.2 + - + +
263A TYR* 1.3 62.5 + - - +
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Residues in contact with TYR 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLU* 6.0 0.9 - - - -
206A TYR* 3.2 7.9 - - - -
207A MET* 2.8 35.9 + - + +
209A VAL* 3.8 24.0 - - + -
257A GLU* 5.1 0.4 - - - -
262A ILE* 1.3 75.9 - - - +
264A GLY* 1.3 89.4 + - - +
265A TYR* 4.8 11.9 - + + -
127B GLU* 3.5 20.8 + - - -
129B LYS* 3.4 37.9 - - - -
130B GLU* 3.7 15.7 + - + -
170B TYR* 4.9 2.9 + - - -
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Residues in contact with GLY 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR* 3.6 9.4 - - - -
206A TYR* 3.6 21.2 - - - -
257A GLU* 4.1 14.5 + - - -
263A TYR* 1.3 97.0 - - - +
265A TYR* 1.3 59.5 + - - -
266A PRO* 3.5 10.8 - - - +
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Residues in contact with TYR 265 (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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62A HIS* 3.9 33.4 - + + +
161A HIS* 4.9 4.2 + + - -
199A GLU* 5.6 2.2 - - - -
203A THR* 3.5 7.1 - - - +
204A LEU 4.2 1.2 + - - -
205A ILE* 2.9 47.2 + - + +
207A MET* 3.3 47.8 - - + +
234A PRO* 4.7 7.9 - - + -
263A TYR* 4.8 9.0 - + - -
264A GLY* 1.3 75.9 - - - -
266A PRO* 1.3 71.4 - - + +
129B LYS* 4.1 13.2 + - - -
172B PRO* 4.0 22.4 + - + -
173B HIS* 4.1 16.8 - + - -
175B ASN* 3.6 18.0 + - - +
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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