Contacts of the strand formed by residues 258 - 263 (chain A) in PDB entry 1QK0
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 VAL 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A TYR* 2.5 25.1 + - - -
206A VAL* 3.4 35.7 - - + -
213A ARG* 5.9 0.2 - - - -
214A THR* 3.3 14.4 - - - +
216A LEU* 4.0 13.2 - - + -
253A LEU* 3.4 25.1 - - + +
255A LEU* 2.9 20.5 + - + +
256A PRO 3.3 0.2 - - - -
257A ASN* 1.3 87.1 - - - +
259A ALA* 1.3 59.8 + - - +
260A MET* 3.8 21.3 - - + -
294A ARG* 5.7 0.2 - - - -
295A ALA* 3.5 9.4 - - + +
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Residues in contact with ALA 259 (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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88A TYR* 3.4 15.0 - - + +
92A PRO* 3.6 33.4 - - + -
213A ARG* 6.0 0.2 - - + -
214A THR 3.0 4.9 + - - +
215A LEU* 3.5 12.4 - - + -
216A LEU* 2.8 27.9 + - - +
258A VAL* 1.3 75.6 - - - +
260A MET* 1.3 63.2 + - - +
261A TYR* 4.3 8.3 - - + -
295A ALA 3.4 3.4 - - - -
297A ARG* 4.9 2.9 - - + -
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Residues in contact with MET 260 (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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216A LEU* 3.4 8.3 - - + -
218A ILE* 3.9 29.8 - - + -
249A ALA 4.2 0.2 - - - +
250A VAL* 3.1 50.9 - - + +
253A LEU* 3.5 31.4 - - - +
254A ASN* 3.7 2.0 - - + +
258A VAL* 3.8 14.6 - - + -
259A ALA* 1.3 73.9 - - - +
261A TYR* 1.3 66.4 + - - +
293A PRO* 5.0 0.2 - - + -
295A ALA* 2.7 30.5 + - + +
296A LEU* 3.6 13.6 - - + +
297A ARG* 3.1 22.9 + - - -
298A GLY 3.5 4.9 + - - -
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Residues in contact with TYR 261 (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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92A PRO* 3.3 20.3 - - + +
93A PHE* 3.5 20.1 - + - -
215A LEU* 5.6 2.7 - - + -
216A LEU 2.8 17.6 + - - +
217A VAL* 3.3 5.1 - - - +
218A ILE* 2.8 26.0 + - - -
259A ALA* 4.3 9.2 - - + -
260A MET* 1.3 78.6 - - - +
262A LEU* 1.3 63.5 + - - +
263A ASP 3.5 0.5 + - - -
297A ARG* 3.2 27.3 - - + +
298A GLY 3.3 6.3 - - - -
299A LEU 3.5 31.4 - - - -
300A ALA* 4.0 2.2 - - + -
346A PHE 4.1 7.6 - - - -
347A PHE 4.1 1.8 - - - -
348A ILE* 3.5 42.8 - - + -
389A ASP* 2.6 27.0 + - - -
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Residues in contact with LEU 262 (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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218A ILE* 3.8 33.9 - - + +
222A SER* 5.8 0.4 - - - +
223A LEU* 3.6 34.5 - - + -
246A ILE* 4.0 11.2 - - + -
250A VAL* 5.0 2.7 - - + -
260A MET 4.2 0.8 - - - -
261A TYR* 1.3 69.9 - - - +
263A ASP* 1.3 65.6 + - - +
264A ALA 3.2 0.3 + - - -
283A PHE* 4.1 9.6 - - + -
286A VAL* 3.9 23.6 - - + -
296A LEU* 4.3 15.9 - - + +
298A GLY 2.8 11.1 + - - +
299A LEU* 3.1 23.1 - - + +
300A ALA 2.8 21.8 + - - -
342A TRP* 4.6 10.3 - - + -
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Residues in contact with ASP 263 (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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217A VAL* 4.7 2.2 - - + -
218A ILE 3.1 12.4 + - - +
219A GLU 3.5 9.3 - - - +
220A PRO* 3.3 33.6 - - + +
221A ASP* 3.4 13.6 + - - -
222A SER* 4.8 1.7 + - - -
223A LEU* 4.7 7.4 + - - +
224A ALA* 4.8 5.2 + - - +
261A TYR 3.5 2.0 + - - -
262A LEU* 1.3 74.6 - - - +
264A ALA* 1.3 59.3 + - - +
265A GLY* 3.1 25.0 + - - +
269A TRP* 5.5 0.5 - - - -
283A PHE* 3.5 15.8 - - - -
300A ALA* 3.6 10.0 - - - +
303A VAL* 3.4 29.6 + - - +
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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