Contacts of the strand formed by residues 274 - 278 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B ILE* 4.1 17.3 - - + -
250B VAL* 3.3 17.7 - - + +
252B ILE* 4.0 16.2 - - + -
264B ILE* 3.7 26.3 - - + +
267B ALA* 4.1 14.4 - - + -
268B ARG* 3.8 38.3 + - + +
272B PRO* 3.1 11.5 + - + +
273B LEU* 1.3 74.1 - - - +
275B PHE* 1.3 74.3 + - - +
327B GLN* 4.4 1.7 + - - +
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Residues in contact with PHE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B PRO* 4.6 0.7 - - + -
250B VAL 2.8 18.8 + - - +
251B TYR* 4.0 22.7 - + + -
252B ILE* 2.7 36.7 + - - +
264B ILE* 4.8 0.2 - - - -
273B LEU* 4.0 23.1 - - + -
274B VAL* 1.3 81.4 - - - +
276B GLY* 1.3 56.8 + - - +
327B GLN* 3.3 22.0 - - + +
328B VAL* 6.3 0.4 - - + -
391B ILE* 3.5 25.4 - - + -
477B HIS* 3.8 26.0 - + - -
478B LEU* 3.5 38.6 - - + -
481B ARG* 4.5 13.2 - - - -
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Residues in contact with GLY 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B TYR* 5.5 0.4 - - - -
252B ILE 3.8 2.7 - - - -
264B ILE* 4.1 14.2 - - - +
274B VAL 4.4 0.2 + - - -
275B PHE* 1.3 74.1 - - - +
277B GLU* 1.3 59.8 + - - -
278B PRO* 3.4 9.7 - - - +
326B LEU* 3.9 19.3 - - - -
327B GLN* 2.9 33.3 + - - +
328B VAL* 3.6 9.5 + - - +
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Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B VAL* 3.4 17.4 - - + +
73B ASN* 2.7 41.3 + - - +
196B LEU* 5.1 1.2 - - - +
251B TYR* 2.5 42.6 + - + +
252B ILE 2.8 18.5 + - - +
253B THR* 3.5 2.1 - - - +
254B LYS* 3.0 24.1 + - - +
255B VAL* 3.0 21.8 + - - +
276B GLY* 1.3 72.6 - - - -
278B PRO* 1.3 67.6 - - - +
279B ILE* 4.1 3.0 - - - +
328B VAL* 3.8 10.5 - - + -
330B GLY 4.4 2.2 - - - +
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Residues in contact with PRO 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B VAL* 3.7 19.3 - - + +
276B GLY 3.4 9.2 - - - +
277B GLU* 1.3 89.0 - - - +
279B ILE* 1.3 61.6 + - - +
282B SER* 4.0 1.6 - - - +
283B LEU* 4.0 30.7 - - + -
317B LEU* 5.0 2.9 - - + -
321B LEU* 4.5 8.1 - - + -
326B LEU* 3.9 33.9 - - + -
328B VAL 3.0 15.9 - - - +
329B THR* 3.4 5.9 - - - -
330B GLY 3.3 16.8 + - - -
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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