Contacts of the strand formed by residues 259 - 263 (chain A) in PDB entry 1QWN
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 LEU 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A PRO* 3.8 29.2 - - + +
216A LEU* 3.9 18.6 - - + -
217A GLN* 4.3 11.7 - - + +
221A PHE* 3.4 29.8 - - + +
222A LYS* 3.5 21.5 - - - +
223A ASN 4.4 0.9 - - - +
224A MET* 3.8 30.5 - - + -
246A LEU* 4.3 2.0 - - - -
247A TRP* 3.0 27.6 + - - +
257A THR 4.4 2.7 - - - +
258A ALA* 1.3 76.3 - - - +
260A PHE* 1.3 71.6 + - - +
261A THR* 3.1 7.0 + - - +
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Residues in contact with PHE 260 (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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222A LYS 3.8 7.3 + - - +
223A ASN* 3.2 30.1 - - - +
224A MET* 2.9 25.5 + - - +
244A GLU* 3.7 38.8 - - + -
245A PHE 3.6 7.9 - - - -
246A LEU* 4.0 24.2 - - + +
259A LEU* 1.3 74.5 - - - +
261A THR* 1.3 63.6 + - - +
383A PHE* 3.7 25.4 - + - -
386A VAL* 3.9 14.6 - - + -
387A HIS* 3.5 18.2 - + + -
390A GLU* 5.7 0.4 - - - -
397A PHE* 3.5 37.9 - + + -
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Residues in contact with THR 261 (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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224A MET* 3.2 25.4 - - + +
226A ILE* 4.2 16.8 - - + -
243A LEU 3.7 1.2 - - - +
244A GLU* 3.2 6.6 - - - +
245A PHE* 2.8 68.6 + - + -
247A TRP* 3.5 22.1 - - + +
259A LEU 3.1 13.3 + - - -
260A PHE* 1.3 75.5 - - - +
262A HIS* 1.3 65.6 + - - +
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Residues in contact with HIS 262 (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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224A MET 2.8 10.1 + - - +
225A LEU* 3.2 23.2 - - + -
226A ILE* 2.9 25.1 + - - +
243A LEU 3.7 2.7 - - - -
244A GLU* 2.8 29.0 + - + +
261A THR* 1.3 76.1 - - - +
263A MET* 1.3 67.7 + - - +
264A MET* 3.8 8.6 - - + +
265A PRO* 5.1 0.6 - - - +
325A LYS* 6.1 2.0 + - - -
329A TYR* 3.4 35.8 + + - -
335A LEU* 3.9 20.2 + - + +
382A TYR* 3.6 14.7 + + - -
383A PHE* 3.9 23.5 - - + -
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Residues in contact with MET 263 (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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226A ILE* 3.5 19.5 - - + +
227A GLN 5.0 0.2 - - - +
229A THR* 3.2 33.2 - - + +
233A VAL* 4.3 3.4 - - + -
234A LYS* 4.2 7.4 - - - +
237A LEU* 3.6 19.3 - - + -
243A LEU* 2.8 46.5 + - + +
245A PHE* 4.0 10.3 - - + -
261A THR* 4.1 1.0 - - - +
262A HIS* 1.3 73.9 - - - +
264A MET* 1.3 66.5 + - - +
329A TYR* 2.8 24.9 + - - -
404A PHE* 3.4 39.0 - - + -
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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