Contacts of the strand formed by residues 287 - 293 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ARG* 3.7 19.1 + - - +
126B VAL* 3.4 2.3 - - - -
127B ARG* 2.9 50.2 + - + +
285B GLY 4.0 0.2 + - - -
286B LEU* 1.3 71.8 - - - +
288B ALA* 1.3 61.7 + - - +
289B GLY* 4.0 1.7 + - - -
315B ARG* 3.4 33.8 - - - +
330B ASP* 2.9 38.0 + - - -
332B SER* 3.2 28.8 + - - -
333B ASN* 3.5 2.2 - - - -
336B ARG* 3.2 32.3 - - - +
400B PO4 2.8 39.3 + - - +
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Residues in contact with ALA 288 (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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125B ARG 3.5 4.9 - - - -
126B VAL* 4.1 19.1 - - + +
241B MET* 4.6 5.4 - - + -
286B LEU* 4.0 15.0 - - + -
287B ARG* 1.3 72.3 - - - +
289B GLY* 1.3 58.2 + - - +
332B SER* 3.1 21.4 - - - -
333B ASN* 2.7 18.5 + - - +
345B VAL* 4.2 12.3 - - + -
348B VAL* 3.5 22.2 - - + +
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Residues in contact with GLY 289 (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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125B ARG* 2.9 40.2 + - - +
241B MET* 3.5 5.6 - - - +
287B ARG* 4.0 2.5 + - - +
288B ALA* 1.3 76.1 - - - +
290B VAL* 1.3 68.9 + - - +
330B ASP* 5.1 2.9 - - - -
331B ILE 2.9 13.5 - - - -
332B SER* 3.9 5.2 - - - -
348B VAL* 4.7 2.7 - - - -
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 3.5 37.5 - - + -
121B VAL* 4.0 7.6 - - + -
123B SER 3.2 8.5 - - - +
124B SER* 3.9 11.0 - - - +
241B MET* 4.0 4.0 - - + -
289B GLY* 1.3 79.9 - - - +
291B HIS* 1.3 65.3 + - - +
292B ILE* 4.0 19.5 - - + -
329B PHE 3.4 0.7 - - - +
330B ASP* 3.4 6.5 + - - +
331B ILE* 3.0 33.8 + - + +
348B VAL* 5.4 0.2 - - + -
352B VAL* 3.9 28.5 - - + -
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Residues in contact with HIS 291 (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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121B VAL* 3.5 3.1 - - - -
122B LEU* 2.7 47.2 + - + +
123B SER* 3.0 31.2 + - - +
290B VAL* 1.3 77.0 - - - +
292B ILE* 1.3 56.4 + - - +
317B THR* 3.8 37.1 + - + +
318B GLY* 5.1 0.8 + - - -
328B VAL* 4.7 2.9 - - + -
329B PHE 3.2 5.8 - - - +
330B ASP* 3.5 33.0 + - - +
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Residues in contact with ILE 292 (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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120B TYR* 3.2 17.3 - - + +
121B VAL* 4.0 10.3 - - + -
122B LEU* 5.4 0.2 - - - -
290B VAL* 4.0 9.9 - - + -
291B HIS* 1.3 75.7 - - - +
293B LYS* 1.3 71.3 + - - +
294B LEU* 3.7 32.5 + - + -
327B GLY 3.3 1.9 - - - +
328B VAL* 3.3 3.7 - - - -
329B PHE* 2.9 36.7 + - + +
331B ILE* 3.8 23.8 - - + -
352B VAL* 4.0 15.0 - - + +
355B LEU* 5.0 2.9 - - + -
356B ILE* 3.7 28.9 - - + -
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Residues in contact with LYS 293 (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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118B GLU 5.3 0.2 + - - -
119B ARG* 2.9 36.8 + - - +
120B TYR* 2.8 35.6 + - + +
122B LEU* 4.1 25.9 - - + +
292B ILE* 1.3 72.8 - - - +
294B LEU* 1.3 70.6 + - - +
295B PRO* 3.5 14.5 - - + +
327B GLY 3.2 5.6 - - - +
328B VAL* 3.8 23.1 - - + -
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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