Contacts of the strand formed by residues 328 - 333 (chain F) in PDB entry 1QK1
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 328 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F LEU* 3.9 27.6 - - + -
291F HIS* 4.7 2.5 - - + -
292F ILE 3.3 8.1 - - - +
293F LYS* 4.2 15.5 - - + -
317F THR* 4.0 27.4 - - + +
324F ALA* 3.3 29.1 - - - +
325F THR* 3.3 19.3 + - + +
326F GLY 4.3 3.8 - - - +
327F GLY* 1.3 80.7 - - - +
329F PHE* 1.3 67.4 + - - +
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Residues in contact with PHE 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290F VAL 3.4 0.9 - - - +
291F HIS* 3.2 9.1 - - - +
292F ILE* 2.9 36.6 + - + +
294F LEU* 4.6 7.4 - - + -
298F SER* 3.6 32.5 - - - -
303F PHE* 4.7 11.4 - + - -
314F LYS* 3.9 33.2 - - + -
315F ARG 3.9 9.0 - - - +
317F THR* 4.6 3.8 - - - -
323F ALA* 5.9 4.3 - - + -
324F ALA* 3.9 22.0 - - + -
327F GLY* 3.5 29.4 - - - -
328F VAL* 1.3 74.5 - - - +
330F ASP* 1.3 60.4 + - - +
331F ILE* 3.8 20.6 + - + -
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Residues in contact with ASP 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287F ARG* 2.9 36.8 + - - -
289F GLY* 5.1 1.2 - - - -
290F VAL 3.4 7.4 + - - +
291F HIS* 3.5 26.8 + - + +
313F GLN* 3.6 1.6 - - - +
314F LYS* 3.3 5.2 - - - -
315F ARG* 3.1 50.5 + - + +
316F GLY 4.1 8.3 - - - +
317F THR 4.6 0.2 - - - +
329F PHE* 1.3 71.8 - - - +
331F ILE* 1.3 67.3 + - - +
332F SER* 4.4 1.0 + - - -
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Residues in contact with ILE 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F GLY* 2.9 22.5 - - - -
290F VAL* 3.0 23.5 + - + +
292F ILE* 3.7 25.4 - - + -
294F LEU* 5.3 1.1 - - + -
303F PHE* 4.9 6.7 - - + -
307F LEU* 4.7 12.3 - - + -
312F LEU* 3.9 33.4 - - + -
313F GLN 3.4 6.1 - - - +
314F LYS* 3.4 30.7 - - + +
329F PHE* 4.0 10.1 - - + -
330F ASP* 1.3 73.6 + - - +
332F SER* 1.3 63.2 + - - +
348F VAL* 5.1 2.0 - - - +
352F VAL* 4.6 6.5 - - + -
355F LEU* 4.3 13.5 - - + -
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Residues in contact with SER 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F ARG* 3.2 44.0 + - - -
288F ALA 3.1 20.6 - - - -
289F GLY* 3.9 1.1 - - - -
312F LEU* 3.4 11.4 - - - -
313F GLN* 2.9 44.5 + - - +
315F ARG* 4.6 0.5 + - - -
330F ASP* 4.2 1.0 + - - -
331F ILE* 1.3 76.7 - - - +
333F ASN* 1.3 62.3 + - - +
348F VAL* 4.4 1.8 - - - -
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Residues in contact with ASN 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286F LEU* 3.0 25.4 + - - +
287F ARG* 3.5 2.4 - - - -
288F ALA* 2.7 36.0 + - - +
311F ARG 4.0 5.4 - - - -
312F LEU* 4.2 0.9 - - - -
313F GLN* 3.4 6.2 + - - -
332F SER* 1.3 75.5 + - - +
334F LEU* 1.3 59.5 + - - +
335F ASP 2.8 27.0 + - - +
336F ARG* 2.9 25.7 + - - +
344F LEU* 4.0 20.8 - - + +
347F LEU* 4.6 7.6 - - + -
348F VAL* 3.6 19.5 - - + +
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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