Contacts of the strand formed by residues 330 - 336 (chain A) in PDB entry 1KCW
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 GLN 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.1 50.1 + - + +
28A VAL* 3.3 18.6 - - - +
29A ASP 5.1 0.2 + - - -
243A VAL* 4.7 5.1 - - - +
246A TYR 5.1 2.1 - - - +
247A THR 4.9 1.2 - - - -
248A PHE* 4.6 1.7 + - - -
249A GLY* 3.2 26.1 + - - +
250A SER 4.5 0.5 + - - -
251A LEU 5.2 0.3 + - - -
316A MET* 3.3 28.0 - - + +
317A LEU 3.5 4.5 - - - -
318A SER* 3.7 14.6 - - - -
325A LEU* 2.6 38.4 + - + +
328A GLY* 3.5 5.5 + - - -
329A LEU* 1.3 88.5 + - - +
331A ALA* 1.3 63.5 + - - +
332A PHE* 5.5 0.4 - - + -
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Residues in contact with ALA 331 (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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243A VAL* 3.7 17.5 - - + -
249A GLY* 4.3 6.0 - - - -
251A LEU* 3.6 34.1 - - + -
254A LEU* 5.0 0.3 - - - +
316A MET* 4.1 1.7 - - - -
317A LEU* 2.9 43.4 + - + +
330A GLN* 1.3 77.5 - - - +
332A PHE* 1.3 67.4 + - - +
333A PHE* 4.2 0.5 - - - +
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Residues in contact with PHE 332 (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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24A LYS* 4.2 7.0 - - + -
25A LEU 4.1 8.5 - - - -
26A ILE* 4.2 14.4 - - + -
249A GLY* 3.5 35.4 + - - +
251A LEU 3.5 19.5 + - - +
254A LEU* 4.0 8.7 - - - +
314A GLU* 6.2 0.7 - - + -
315A TRP 3.8 19.3 - - - +
316A MET* 4.3 11.2 - - - +
330A GLN* 5.5 0.2 - - + -
331A ALA* 1.3 76.5 - - - +
333A PHE* 1.3 61.0 + - - +
472A TYR* 3.7 26.2 - + + -
474A PRO* 3.5 65.1 - - + +
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Residues in contact with PHE 333 (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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254A LEU* 3.3 39.3 - - + +
256A MET* 3.3 25.8 - - + -
264A TRP* 4.6 5.2 - + - -
280A PHE* 4.4 26.0 - + + -
282A GLY 4.6 3.1 - - - -
283A GLN* 4.5 18.2 - - + -
307A MET* 5.1 2.9 - - - -
314A GLU* 4.1 0.3 - - - -
315A TRP* 3.2 39.2 + + + +
316A MET 3.3 41.3 - - - -
317A LEU* 3.8 13.0 - - + -
332A PHE* 1.3 75.5 - - - +
334A GLN* 1.3 66.0 + - - +
335A VAL* 4.6 7.9 - - + -
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Residues in contact with GLN 334 (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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254A LEU 2.9 15.3 + - - +
255A SER* 3.4 12.0 + - - -
256A MET* 2.9 29.9 + - - +
313A GLY 3.6 13.4 - - - +
314A GLU* 4.1 16.4 - - + +
333A PHE* 1.3 82.1 - - - +
335A VAL* 1.3 65.0 + - - +
336A GLN* 3.4 32.9 + - - +
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Residues in contact with VAL 335 (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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256A MET* 3.2 15.9 - - + -
257A CYS 3.3 8.1 - - - +
258A ALA* 3.3 38.6 - - + +
283A GLN* 3.7 20.4 - - - +
309A ALA* 3.4 26.7 - - + -
310A GLN 4.4 2.7 - - - +
311A ASN 4.8 0.9 - - - +
312A PRO* 3.2 15.1 - - + +
313A GLY* 2.9 30.5 + - - +
315A TRP* 4.7 1.5 - - + -
333A PHE* 4.6 4.9 - - + -
334A GLN* 1.3 74.8 - - - +
336A GLN* 1.3 61.9 + - - +
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Residues in contact with GLN 336 (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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196A ARG* 5.8 2.4 - - - +
255A SER* 3.9 18.6 + - - +
256A MET 2.8 11.7 + - - +
257A CYS* 4.2 4.4 - - - -
258A ALA 3.0 21.3 + - - -
334A GLN* 3.4 27.3 - - - +
335A VAL* 1.3 73.5 - - - +
337A GLU* 1.3 62.9 + - - +
338A CYS* 3.0 31.8 + - - -
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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