Contacts of the strand formed by residues 287 - 293 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125G ARG* 3.7 20.0 + - - +
126G VAL* 3.5 2.8 - - - -
127G ARG* 2.9 52.2 + - + +
285G GLY 4.0 0.2 + - - -
286G LEU* 1.3 72.0 - - - +
288G ALA* 1.3 61.7 + - - +
289G GLY* 3.9 1.2 + - - -
313G GLN* 4.5 0.2 - - - +
315G ARG* 3.4 31.6 - - - +
330G ASP* 2.9 38.4 + - - -
332G SER* 3.2 29.0 + - - -
333G ASN* 3.5 2.0 - - - -
336G ARG* 3.2 31.4 - - - +
400G PO4 2.8 39.7 + - - +
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Residues in contact with ALA 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G ARG 3.5 4.9 - - - -
126G VAL* 4.1 17.7 - - + +
241G MET* 4.5 5.4 - - + -
286G LEU* 4.0 14.7 - - + -
287G ARG* 1.3 72.3 - - - +
289G GLY* 1.3 59.5 + - - +
332G SER* 3.1 21.3 - - - -
333G ASN* 2.7 18.3 + - - +
345G VAL* 4.2 13.0 - - + -
348G VAL* 3.5 22.3 - - + +
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Residues in contact with GLY 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G ARG* 2.9 39.7 + - - +
241G MET* 3.5 6.6 - - - +
287G ARG* 3.9 2.3 + - - -
288G ALA* 1.3 76.5 - - - +
290G VAL* 1.3 69.0 + - - +
330G ASP* 5.0 2.7 - - - -
331G ILE 2.9 13.5 - - - -
332G SER* 3.9 5.2 - - - -
348G VAL* 4.7 2.7 - - - -
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Residues in contact with VAL 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G PHE* 3.5 37.0 - - + -
121G VAL* 4.0 9.6 - - + -
123G SER 3.2 13.5 - - - +
124G SER* 3.9 5.4 - - - +
241G MET* 4.0 3.6 - - + -
289G GLY* 1.3 80.8 - - - +
291G HIS* 1.3 65.2 + - - +
292G ILE* 4.1 19.1 - - + -
329G PHE 3.4 0.7 - - - +
330G ASP* 3.4 6.4 + - - +
331G ILE* 2.9 34.3 + - + +
348G VAL* 5.4 0.2 - - + -
352G VAL* 3.9 26.2 - - + -
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Residues in contact with HIS 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G VAL* 3.5 3.5 - - - +
122G LEU* 2.7 45.4 + - + +
123G SER* 3.0 31.0 + - - +
290G VAL* 1.3 78.4 - - - +
292G ILE* 1.3 58.6 + - - +
317G THR* 4.0 36.4 + - + +
328G VAL* 4.7 3.1 - - + +
329G PHE 3.2 5.8 - - - +
330G ASP* 3.5 31.2 + - + +
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Residues in contact with ILE 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G TYR 3.2 16.4 - - - +
121G VAL* 4.0 7.4 - - + -
290G VAL* 4.1 9.2 - - + -
291G HIS* 1.3 75.4 - - - +
293G LYS* 1.3 64.0 + - - +
294G LEU* 3.6 39.4 + - + -
327G GLY 3.3 4.2 - - - +
328G VAL* 3.3 2.8 - - - -
329G PHE* 2.9 37.6 + - + +
331G ILE* 3.7 30.1 - - + -
352G VAL* 4.0 28.7 - - + +
355G LEU* 4.9 3.8 - - + -
356G ILE* 4.1 12.1 - - + -
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Residues in contact with LYS 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G GLU 5.5 0.6 + - - -
119G ARG* 3.2 29.3 + - - +
120G TYR* 2.7 28.8 + - + +
122G LEU* 3.7 33.4 - - + +
292G ILE* 1.3 69.2 - - - +
294G LEU* 1.3 70.9 + - - +
295G PRO* 3.5 10.8 - - + +
325G THR* 5.9 2.5 - - + -
327G GLY 3.3 6.1 - - - +
328G VAL* 3.8 22.4 - - + -
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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