Contacts of the strand formed by residues 250 - 255 (chain A) in PDB entry 1KCX
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 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A PHE* 4.0 17.9 - - + -
195A ILE* 3.8 6.1 - - + +
197A VAL* 3.9 24.7 - - + -
239A ALA* 4.4 6.3 - - + +
240A ILE* 4.6 10.1 - - + -
243A ALA* 3.6 23.1 - - + -
249A PRO* 1.3 77.0 - - - +
251A TYR* 1.3 62.2 + - - +
252A ILE* 4.6 8.5 - - + -
272A PRO* 6.1 0.9 - - + -
273A LEU 3.0 10.6 + - - +
274A VAL* 3.3 27.3 - - + +
275A PHE* 3.0 26.6 + - - -
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Residues in contact with TYR 251 (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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72A VAL* 3.2 22.0 + - - +
194A VAL* 4.5 8.1 - - + -
195A ILE 2.8 21.1 + - - +
196A LEU* 3.4 19.3 - - + -
197A VAL* 3.0 28.9 + - - +
250A VAL* 1.3 73.9 - - - +
252A ILE* 1.3 65.3 + - - +
253A THR* 3.8 13.9 - - + -
275A PHE* 3.8 23.8 - + + +
277A GLU* 2.7 48.6 + - + +
328A VAL* 3.5 13.6 - - + +
391A ILE* 4.4 15.9 - - + -
392A PHE* 3.7 28.9 - + - -
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Residues in contact with ILE 252 (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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197A VAL* 4.3 15.0 - - + +
199A ALA* 4.8 7.9 - - + -
232A GLU* 5.9 1.3 - - - +
236A VAL* 4.0 44.6 - - + +
239A ALA* 4.5 14.8 - - + -
240A ILE* 5.0 1.3 - - + -
250A VAL* 4.6 8.5 - - + -
251A TYR* 1.3 77.2 - - - +
253A THR* 1.3 71.8 + - - +
255A VAL* 3.6 14.8 - - + +
264A ILE* 4.0 13.5 - - + -
274A VAL* 4.1 11.4 - - + -
275A PHE 2.9 18.8 + - - +
277A GLU* 3.0 26.9 + - - +
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Residues in contact with THR 253 (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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73A ASN* 4.1 9.4 - - - +
165A GLN* 3.6 23.1 + - - +
196A LEU* 3.8 27.6 - - + -
197A VAL 2.7 27.6 + - - +
198A HIS* 3.9 6.4 - - - +
199A ALA 5.3 2.6 + - - -
232A GLU* 5.5 0.2 - - - +
251A TYR* 3.8 13.0 - - + -
252A ILE* 1.3 80.7 - - - +
254A LYS* 1.3 78.1 + - - +
255A VAL 3.3 1.0 + - - -
277A GLU* 3.6 13.7 - - - +
305A PRO* 5.3 1.9 - - - +
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Residues in contact with LYS 254 (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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73A ASN* 3.7 22.2 - - - +
75A TYR* 4.7 18.7 - - - -
78A LYS* 5.1 10.7 - - - +
165A GLN* 6.0 1.1 - - - +
170A TYR* 5.8 0.2 + - - -
198A HIS* 4.2 18.8 + - - -
232A GLU* 3.7 1.6 - - - +
253A THR* 1.3 78.1 - - - +
255A VAL* 1.3 64.7 + - - +
256A MET* 3.1 19.7 + - + +
277A GLU* 3.0 18.7 + - - +
279A ILE* 4.0 23.1 - - + -
303A THR* 4.7 9.5 + - - +
304A SER 2.9 27.5 + - - +
305A PRO* 3.4 23.3 - - + +
332A GLY* 4.7 11.6 + - - +
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Residues in contact with VAL 255 (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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232A GLU* 3.8 4.7 - - - -
252A ILE* 3.6 24.7 - - + +
253A THR 4.2 0.4 - - - -
254A LYS* 1.3 69.8 - - - +
256A MET* 1.3 71.7 + - - +
257A SER 4.2 6.5 - - - +
260A ALA* 4.4 6.3 - - + -
261A ALA* 4.1 33.0 - - + +
264A ILE* 3.9 11.7 - - + -
276A GLY* 4.2 1.6 - - - -
277A GLU 3.1 32.5 + - - +
278A PRO* 3.6 11.9 - - + +
282A SER* 3.0 10.2 + - - -
317A LEU* 3.9 9.6 - - + +
326A LEU* 4.6 7.4 - - + -
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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