Contacts of the strand formed by residues 274 - 278 (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 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ILE* 3.9 26.7 - - + -
250A VAL* 3.3 19.7 - - + +
252A ILE* 4.1 9.9 - - + -
264A ILE* 4.0 14.2 - - + +
267A ALA* 3.9 24.9 - - + -
268A ARG* 4.0 30.7 + - + +
272A PRO* 3.1 14.6 + - + +
273A LEU* 1.3 74.1 - - - +
275A PHE* 1.3 76.3 + - - +
327A GLN* 4.6 1.0 + - - +
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 6.5 0.2 - - + -
249A PRO* 4.6 2.7 - - + -
250A VAL 3.0 18.1 + - - +
251A TYR* 4.2 22.9 - + + -
252A ILE* 2.9 32.1 + - - +
264A ILE* 4.5 1.7 - - - +
273A LEU* 4.0 21.8 - - + -
274A VAL* 1.3 79.7 - - - +
276A GLY* 1.3 58.6 + - - +
327A GLN* 3.3 23.6 - - + +
328A VAL* 6.1 0.9 - - + -
391A ILE* 3.7 24.9 - - + -
477A HIS* 4.0 25.4 - + - -
478A LEU* 3.6 37.7 - - + -
481A ARG* 4.7 11.7 - - - -
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Residues in contact with GLY 276 (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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251A TYR* 5.6 0.4 - - - -
252A ILE 3.9 2.7 - - - -
264A ILE* 4.1 11.3 - - - +
275A PHE* 1.3 75.8 - - - +
277A GLU* 1.3 59.3 + - - -
278A PRO* 3.3 11.0 - - - +
326A LEU* 3.9 17.9 - - - -
327A GLN* 2.8 35.3 + - - +
328A VAL* 3.6 9.7 + - - +
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Residues in contact with GLU 277 (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 21.2 - - + +
73A ASN* 2.7 41.4 + - - +
196A LEU* 5.4 1.0 - - - +
251A TYR* 2.7 41.8 + - + +
252A ILE 3.0 17.5 + - - +
253A THR* 3.6 1.7 - - - +
254A LYS* 3.0 25.0 + - - +
255A VAL* 3.1 20.5 + - - +
276A GLY* 1.3 72.3 - - - -
278A PRO* 1.3 68.9 - - - +
279A ILE* 4.0 3.2 - - - +
328A VAL* 3.7 7.6 - - + -
330A GLY 4.4 3.4 - - - +
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Residues in contact with PRO 278 (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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255A VAL* 3.6 20.4 - - + +
276A GLY 3.3 10.5 - - - +
277A GLU* 1.3 88.5 - - - +
279A ILE* 1.3 59.9 + - - +
282A SER* 4.2 1.8 - - - +
283A LEU* 4.1 28.9 - - + -
317A LEU* 4.9 2.7 - - + -
321A LEU* 4.3 13.5 - - + -
326A LEU* 4.0 29.8 - - + -
328A VAL 3.1 15.0 - - - +
329A THR* 3.5 4.4 - - + -
330A GLY 3.2 18.0 + - - -
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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