Contacts of the strand formed by residues 287 - 293 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D ARG* 3.7 18.5 + - - +
126D VAL* 3.5 2.3 - - - -
127D ARG* 3.0 53.4 + - + +
285D GLY 4.0 0.4 + - - -
286D LEU* 1.3 71.2 - - - +
288D ALA* 1.3 61.1 + - - +
289D GLY* 4.0 1.3 + - - -
313D GLN* 4.5 0.2 - - - +
315D ARG* 3.4 34.6 - - - +
330D ASP* 2.9 38.2 + - - -
332D SER* 3.2 28.8 + - - -
333D ASN* 3.5 2.7 - - - -
336D ARG* 3.2 31.2 - - - +
400D PO4 2.9 38.6 + - - +
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Residues in contact with ALA 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ARG 3.4 5.4 - - - -
126D VAL* 4.1 17.9 - - + +
241D MET* 4.5 5.4 - - + -
286D LEU* 4.0 15.2 - - + -
287D ARG* 1.3 73.2 - - - +
289D GLY* 1.3 58.5 + - - +
332D SER* 3.1 22.1 - - - -
333D ASN* 2.7 19.3 + - - +
345D VAL* 4.2 12.6 - - + -
348D VAL* 3.5 21.6 - - + +
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Residues in contact with GLY 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ARG* 2.9 40.4 + - - +
241D MET* 3.5 6.3 - - - +
287D ARG* 4.0 1.9 + - - -
288D ALA* 1.3 75.6 - - - +
290D VAL* 1.3 68.1 + - - +
330D ASP* 5.1 3.1 - - - -
331D ILE 3.0 13.9 - - - -
332D SER* 3.9 4.5 - - - -
348D VAL* 4.7 3.4 - - - -
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Residues in contact with VAL 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D PHE* 3.6 35.2 - - + -
121D VAL* 3.9 8.3 - - + -
123D SER 3.2 14.8 - - - +
124D SER* 3.9 8.1 - - - +
241D MET* 4.0 3.6 - - + -
289D GLY* 1.3 79.2 - - - +
291D HIS* 1.3 64.4 - - - +
292D ILE* 4.1 19.5 - - + -
329D PHE 3.4 0.7 - - - +
330D ASP* 3.4 6.5 + - - +
331D ILE* 3.0 34.1 + - + +
348D VAL* 5.4 0.7 - - + -
352D VAL* 3.9 27.1 - - + -
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Residues in contact with HIS 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D VAL* 3.5 3.3 - - - -
122D LEU* 2.8 47.0 + - + +
123D SER* 3.0 28.8 + - - +
290D VAL* 1.3 79.9 - - - +
292D ILE* 1.3 58.9 + - - +
317D THR* 3.2 42.3 + - + +
328D VAL* 4.8 2.5 - - + -
329D PHE 3.2 3.8 - - - +
330D ASP* 3.5 31.3 + - + +
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Residues in contact with ILE 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D TYR* 3.2 17.9 - - + +
121D VAL* 4.0 9.9 - - + -
122D LEU* 5.3 0.4 - - - -
290D VAL* 4.1 9.9 - - + -
291D HIS* 1.3 75.9 - - - +
293D LYS* 1.3 63.1 + - - +
294D LEU* 3.5 42.7 + - + -
327D GLY 3.3 3.8 - - - +
328D VAL* 3.3 4.7 - - - +
329D PHE* 2.9 35.2 + - + +
331D ILE* 3.7 24.0 - - + -
352D VAL* 4.1 13.2 - - + +
355D LEU* 4.9 4.5 - - + -
356D ILE* 3.8 25.8 - - + -
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Residues in contact with LYS 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ARG* 3.7 22.5 + - - +
120D TYR* 2.7 31.1 + - + +
122D LEU* 3.7 33.4 - - + +
292D ILE* 1.3 69.1 - - - +
294D LEU* 1.3 67.7 + - - +
295D PRO* 3.2 16.3 - - + +
326D GLY 5.5 1.3 - - - +
327D GLY 3.3 4.3 - - - +
328D VAL* 3.7 22.2 - - + -
359D GLU* 4.5 0.2 - - - +
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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