Contacts of the strand formed by residues 322 - 328 (chain B) in PDB entry 3KSA
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 GLN 322 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237B VAL* 5.1 6.7 - - + -
238B VAL 3.3 11.7 - - - +
239B ARG* 4.3 8.5 - - + -
316B PHE* 3.4 38.1 + - + +
317B LYS 5.1 0.5 - - - +
319B THR 3.3 15.8 + - - +
321B LEU* 1.3 80.2 - - - +
323B ILE* 1.3 65.4 + - - +
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Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B VAL* 3.6 7.0 - - - +
238B VAL* 2.9 34.2 + - + +
260B PRO* 3.4 26.4 - - + +
261B TYR 4.0 14.6 - - - +
263B ILE* 4.5 7.6 - - + -
320B ASP* 3.6 33.7 - - + +
322B GLN* 1.3 78.6 - - - +
324B ASN* 1.3 82.5 + - - +
325B TYR* 5.6 4.0 - - + -
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Residues in contact with ASN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ARG* 5.0 8.7 - - + -
236B VAL 3.0 20.2 - - - +
237B VAL* 4.2 15.1 - - - +
323B ILE* 1.3 92.0 - - - +
325B TYR* 1.3 61.0 + - - +
326B ASN* 4.1 10.8 + - - +
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Residues in contact with TYR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B THR* 4.9 1.4 - - - +
177B ASP* 3.7 11.3 + - - +
178B ILE 3.3 14.9 + - - -
179B PRO* 3.0 46.3 - - + +
213B PHE* 4.0 16.4 - + + -
234B GLY 3.9 0.3 - - - +
235B ARG* 3.6 1.6 - - - -
236B VAL* 2.9 35.1 + - + +
238B VAL* 4.3 20.3 - - + +
261B TYR* 4.0 29.5 - + + -
262B GLU* 4.2 17.1 + - + -
323B ILE* 4.6 5.1 - - + +
324B ASN* 1.3 74.7 - - - +
326B ASN* 1.3 82.1 + - - +
327B PHE* 3.7 15.9 - + - -
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Residues in contact with ASN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ASP* 3.7 14.9 - - + +
234B GLY 3.3 5.1 - - - +
235B ARG* 3.1 27.2 - - - +
324B ASN* 4.1 12.5 + - - +
325B TYR* 1.3 96.8 - - - +
327B PHE* 1.3 65.6 + - - +
328B ASN* 3.9 1.1 - - + -
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Residues in contact with PHE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ASP 4.1 3.4 - - - -
179B PRO* 3.2 26.9 - - + -
211B PRO* 3.4 31.4 - - + -
225B ILE* 5.1 3.4 - - + -
228B ALA* 3.4 27.8 - - + -
229B TYR* 4.2 20.2 - + - -
232B GLY 3.5 6.5 - - - +
233B LYS* 3.1 23.6 - - - +
234B GLY 2.7 31.4 + - - +
236B VAL* 3.8 26.9 - - + -
325B TYR* 3.7 18.6 - + - -
326B ASN* 1.3 78.5 - - - +
328B ASN* 1.3 61.0 - - - +
329B MET* 5.1 5.2 - - + +
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Residues in contact with ASN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ALA* 3.0 28.1 + - - +
176B THR* 3.2 3.7 + - - -
177B ASP* 2.9 39.9 + - + +
232B GLY 3.4 1.1 - - - -
233B LYS* 3.3 27.5 - - - +
326B ASN* 3.8 2.3 + - + -
327B PHE* 1.3 74.0 - - - +
329B MET* 1.3 59.2 + - - +
330B VAL* 3.1 10.6 + - - +
339B GLN* 3.3 17.4 - - - +
630D ARG* 5.7 3.9 + - - +
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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