Contacts of the strand formed by residues 274 - 278 (chain B) in PDB entry 2K7A
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 THR 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B VAL* 3.0 5.6 - - - +
265B ARG* 2.7 73.0 + - - +
267B SER* 3.2 12.0 + - - -
273B TYR* 1.3 79.6 + - - +
275B VAL* 1.3 73.3 + - - +
276B SER 3.6 0.4 + - - +
291B HIS* 4.5 15.0 - - + +
292B TYR 4.2 10.5 - - - +
293B HIS* 3.3 25.2 + - + +
294B ILE* 4.5 0.7 - - - -
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 4.9 1.1 - - + -
263B MET 3.4 11.9 - - - +
264B VAL* 4.1 8.3 - - + -
274B THR* 1.3 76.3 - - - +
276B SER* 1.3 60.1 + - - +
277B VAL* 3.2 23.2 + - + +
290B LYS 3.2 0.5 - - - +
292B TYR* 3.1 46.3 + - + +
294B ILE* 3.9 25.1 - - + -
306B VAL* 5.4 4.5 - - + -
315B ILE* 5.4 2.2 - - + -
318B LEU* 5.8 3.4 - - + -
319B ILE* 3.9 25.4 - - + -
329B LEU* 6.4 1.6 - - + -
333B LEU* 4.6 9.2 - - + -
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Residues in contact with SER 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA* 4.2 8.7 - - - +
253B LEU* 3.7 24.5 - - - +
262B PHE* 3.5 1.9 - - - -
263B MET* 2.6 46.2 + - - -
264B VAL* 4.8 2.5 - - - -
265B ARG* 3.1 30.3 + - - +
274B THR 3.6 2.2 + - - -
275B VAL* 1.3 69.2 - - - +
277B VAL* 1.3 57.9 + - - +
289B ILE* 4.7 5.2 - - - -
290B LYS 3.7 4.9 - - - -
291B HIS* 3.9 10.5 + - - -
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLY 5.0 0.7 - - - +
261B ALA 4.0 5.2 - - - +
262B PHE* 4.3 13.7 - - + +
275B VAL* 3.7 19.3 - - + +
276B SER* 1.3 74.5 - - - +
278B PHE* 1.3 61.0 + - - +
279B THR* 4.0 10.4 + - + +
288B CYS 4.3 0.2 - - - +
289B ILE* 4.5 1.3 - - - -
290B LYS* 2.7 45.9 + - + +
292B TYR* 3.6 26.9 - - + -
329B LEU* 4.4 17.3 - - + -
330B VAL* 4.6 1.6 - - + -
331B THR* 3.7 23.1 - - - +
333B LEU* 4.6 4.9 - - + -
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Residues in contact with PHE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 2.9 50.7 - - + -
254B LEU* 4.2 4.9 - - - -
257B GLY* 3.4 28.5 - - - -
258B LYS 3.7 11.6 - - - +
260B GLY 3.6 1.6 + - - -
261B ALA* 2.7 57.1 + - + +
276B SER 3.9 1.2 + - - -
277B VAL* 1.3 71.6 - - - +
279B THR* 1.3 77.6 + - - +
280B LYS* 3.4 27.4 - - + -
287B PRO* 3.4 28.9 - - + -
288B CYS 3.4 14.4 - - - -
289B ILE* 3.8 14.8 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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