Contacts of the strand formed by residues 287 - 293 (chain A) 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 ARG 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A ARG* 3.6 20.3 + - - +
126A VAL* 3.5 2.4 - - - -
127A ARG* 2.9 48.3 + - + +
285A GLY 4.0 0.2 + - - -
286A LEU* 1.3 72.2 - - - +
288A ALA* 1.3 60.6 + - - +
289A GLY* 3.9 1.9 + - - -
315A ARG* 3.3 31.6 - - - +
330A ASP* 2.9 38.6 + - - -
332A SER* 3.3 29.3 + - - -
333A ASN* 3.5 2.2 - - - -
336A ARG* 3.2 31.6 - - - +
400A PO4 2.7 44.1 + - - +
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Residues in contact with ALA 288 (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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125A ARG 3.4 5.2 - - - -
126A VAL* 4.2 16.4 - - + +
241A MET* 4.5 6.3 - - + -
286A LEU* 4.0 15.2 - - + -
287A ARG* 1.3 72.4 - - - +
289A GLY* 1.3 58.5 + - - +
332A SER* 3.1 20.9 - - - -
333A ASN* 2.7 19.3 + - - +
345A VAL* 4.2 13.0 - - + -
348A VAL* 3.5 22.5 - - + +
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Residues in contact with GLY 289 (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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125A ARG* 2.9 39.4 + - - +
241A MET* 3.5 6.9 - - - +
287A ARG* 3.9 2.3 + - - -
288A ALA* 1.3 75.8 - - - +
290A VAL* 1.3 68.8 + - - +
330A ASP* 5.1 2.9 - - - -
331A ILE 2.9 13.0 - - - -
332A SER* 3.9 4.9 - - - -
348A VAL* 4.7 2.9 - - - -
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Residues in contact with VAL 290 (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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116A PHE* 3.5 35.0 - - + -
121A VAL* 4.0 8.7 - - + -
123A SER 3.2 8.3 - - - +
124A SER* 3.8 13.2 - - - +
241A MET* 4.0 3.6 - - + -
289A GLY* 1.3 79.9 - - - +
291A HIS* 1.3 64.8 + - - +
292A ILE* 4.1 19.1 - - + -
329A PHE 3.4 1.6 - - - +
330A ASP* 3.4 5.1 + - - +
331A ILE* 2.9 36.3 + - + +
348A VAL* 5.4 0.7 - - + -
352A VAL* 3.9 26.9 - - + -
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Residues in contact with HIS 291 (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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121A VAL* 3.4 3.5 - - - -
122A LEU* 2.7 48.2 + - + +
123A SER* 3.0 30.3 + - - +
290A VAL* 1.3 78.8 - - - +
292A ILE* 1.3 55.2 + - - +
317A THR* 3.6 38.0 + - + +
328A VAL* 4.7 2.7 - - + -
329A PHE 3.2 5.2 - - - +
330A ASP* 3.5 32.5 + - + +
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Residues in contact with ILE 292 (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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120A TYR* 3.2 20.0 - - + +
121A VAL* 4.0 4.0 - - + -
122A LEU* 5.4 0.9 - - - -
290A VAL* 4.1 9.2 - - + -
291A HIS* 1.3 75.0 - - - +
293A LYS* 1.3 62.1 + - - +
294A LEU* 3.7 35.3 + - + -
327A GLY 3.3 2.8 - - - +
328A VAL* 3.3 5.2 - - - +
329A PHE* 2.9 36.0 + - + +
331A ILE* 3.7 29.4 - - + -
352A VAL* 4.0 21.1 - - + +
355A LEU* 5.0 4.0 - - + -
356A ILE* 3.9 25.1 - - + -
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Residues in contact with LYS 293 (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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119A ARG 3.9 19.7 + - - +
120A TYR* 2.8 32.9 + - + +
122A LEU* 4.0 30.0 - - + +
292A ILE* 1.3 70.7 - - - +
294A LEU* 1.3 69.9 + - - +
295A PRO* 3.4 17.9 - - + +
326A GLY 5.7 0.2 - - - +
327A GLY 3.1 5.8 - - - +
328A VAL* 3.8 24.7 - - + -
359A GLU* 4.2 0.5 - - - +
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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