Contacts of the strand formed by residues 287 - 293 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H ARG* 3.6 19.6 + - - +
126H VAL* 3.5 2.8 - - - -
127H ARG* 2.9 51.2 + - + +
285H GLY 4.0 0.2 + - - -
286H LEU* 1.3 72.7 - - - +
288H ALA* 1.3 60.8 + - - +
289H GLY* 4.0 1.8 + - - -
313H GLN* 4.4 0.2 - - - +
315H ARG* 3.4 35.2 - - - +
330H ASP* 2.9 38.0 + - - -
332H SER* 3.2 29.2 + - - -
333H ASN* 3.5 2.2 - - - -
336H ARG* 3.2 32.1 - - - +
400H PO4 2.9 39.1 + - - +
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Residues in contact with ALA 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H ARG 3.4 5.2 - - - -
126H VAL* 4.2 16.4 - - + +
241H MET* 4.5 5.4 - - + -
286H LEU* 4.0 15.2 - - + -
287H ARG* 1.3 73.6 - - - +
289H GLY* 1.3 58.1 + - - +
332H SER* 3.1 20.9 - - - -
333H ASN* 2.6 18.9 + - - +
345H VAL* 4.2 13.0 - - + -
348H VAL* 3.5 22.0 - - + +
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Residues in contact with GLY 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H ARG* 2.9 39.9 + - - +
241H MET* 3.5 7.0 - - - +
287H ARG* 4.0 2.3 + - - -
288H ALA* 1.3 74.8 - - - +
290H VAL* 1.3 69.6 + - - +
330H ASP* 5.1 2.9 - - - -
331H ILE 3.0 13.0 - - - -
332H SER* 3.9 5.2 - - - -
348H VAL* 4.7 2.9 - - - -
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Residues in contact with VAL 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H PHE* 3.6 36.8 - - + -
121H VAL* 4.0 8.3 - - + -
123H SER 3.2 13.5 - - - +
124H SER* 3.9 5.4 - - - +
241H MET* 4.1 4.3 - - + -
289H GLY* 1.3 80.6 - - - +
291H HIS* 1.3 64.3 + - - +
292H ILE* 4.1 18.8 - - + -
329H PHE 3.4 0.7 - - - +
330H ASP* 3.4 6.5 + - - +
331H ILE* 3.0 35.3 + - + +
352H VAL* 3.9 28.0 - - + -
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Residues in contact with HIS 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 3.5 3.1 - - - -
122H LEU* 2.7 44.9 + - + +
123H SER* 3.0 31.4 + - - +
290H VAL* 1.3 78.1 - - - +
292H ILE* 1.3 59.2 + - - +
317H THR* 3.4 36.3 - - + +
328H VAL* 4.8 2.7 - - + +
329H PHE 3.2 4.0 - - - +
330H ASP* 3.6 32.6 + - + +
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Residues in contact with ILE 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120H TYR* 3.2 18.2 - - + +
121H VAL* 4.0 4.3 - - + -
122H LEU* 5.3 0.7 - - - -
290H VAL* 4.1 8.5 - - + -
291H HIS* 1.3 75.7 - - - +
293H LYS* 1.3 61.4 + - - +
294H LEU* 3.6 32.3 + - + -
327H GLY 3.2 4.3 - - - +
328H VAL* 3.3 5.1 - - - -
329H PHE* 2.9 39.9 + - + +
331H ILE* 3.7 30.1 - - + -
352H VAL* 4.0 20.6 - - + +
355H LEU* 4.9 3.1 - - + -
356H ILE* 3.8 28.3 - - + -
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Residues in contact with LYS 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H ARG* 3.5 23.8 + - - +
120H TYR* 2.6 36.3 + - + +
122H LEU* 4.2 30.3 - - + +
292H ILE* 1.3 69.4 - - - +
294H LEU* 1.3 69.9 + - - +
295H PRO* 3.3 14.3 - - + +
326H GLY 5.5 1.1 - - - +
327H GLY 3.4 5.6 - - - +
328H VAL* 4.2 15.9 - - + +
359H GLU* 4.5 0.3 - - - +
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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