Contacts of the strand formed by residues 258 - 263 (chain B) in PDB entry 3QKJ
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 MET 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B TYR* 3.7 9.7 - - - -
219B ASP* 4.4 0.2 - - - +
254B ALA* 3.7 3.0 - - + +
255B MET* 2.9 39.4 + - + +
256B SER 4.2 2.7 - - - +
257B GLY* 1.4 81.7 - - - +
259B ARG* 1.3 78.9 + - - +
271B GLU* 3.7 51.4 - - + +
272B VAL 3.4 5.4 - - - +
273B SER* 3.6 28.9 - - - +
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Residues in contact with ARG 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TYR* 3.5 44.0 + - - +
219B ASP* 2.7 43.0 + - - -
221B LYS* 3.1 16.2 + - - +
222B GLU 3.1 19.4 + - - +
223B PHE* 2.7 28.8 + - + -
243B VAL* 4.2 9.4 - - + -
254B ALA* 4.5 2.0 - - - -
257B GLY 4.3 1.8 - - - -
258B MET* 1.3 92.1 + - - +
260B TRP* 1.3 68.6 + - - +
261B VAL* 3.7 1.1 + - + +
270B SER 3.6 0.3 - - - +
271B GLU* 3.5 2.7 - - - -
272B VAL* 2.8 32.5 + - - +
274B ALA* 4.7 6.5 - - + -
277B LEU* 3.9 28.3 - - + -
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Residues in contact with TRP 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B SO4 3.9 22.2 - - - -
217B TYR* 2.9 16.4 + - - +
243B VAL* 3.5 8.0 - - - +
244B VAL* 3.0 30.6 + - + +
245B SER 4.7 0.2 - - - +
246B TRP* 3.5 22.0 - - + +
249B THR* 3.8 27.6 - - + -
251B LYS* 3.8 28.0 - - + -
252B ARG* 2.8 43.5 + - + -
254B ALA* 3.4 25.5 - - + +
259B ARG* 1.3 74.5 - - - +
261B VAL* 1.3 59.5 + - - +
269B PHE* 4.2 9.9 - - + -
270B SER* 3.4 30.3 - - - -
271B GLU* 3.5 26.9 - - + -
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B VAL* 4.3 4.9 - - + -
241B ALA* 3.9 12.8 - - + -
242B MET 3.3 7.9 - - - +
243B VAL* 4.2 12.6 - - + -
244B VAL* 4.3 4.3 - - - +
259B ARG 4.3 4.9 - - - +
260B TRP* 1.3 78.0 - - - +
262B GLN* 1.3 59.8 + - - +
263B TRP* 3.9 24.6 + - + +
268B LYS 3.9 0.3 - - - +
269B PHE* 3.3 6.1 - - - +
270B SER 2.9 39.8 + - - +
272B VAL* 3.9 16.8 - - + -
277B LEU* 3.9 34.5 - - + -
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Residues in contact with GLN 262 (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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241B ALA* 3.3 4.1 - - - -
242B MET* 2.8 33.9 + - + +
244B VAL* 4.0 17.1 - - + +
261B VAL* 1.3 72.1 - - - +
263B TRP* 1.3 61.6 - - - +
264B PHE* 3.7 1.2 + - - -
267B GLY* 3.0 40.3 + - - +
268B LYS 3.3 5.8 - - - +
269B PHE* 3.5 33.1 - - + -
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Residues in contact with TRP 263 (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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231B GLY* 3.6 31.2 - - - -
233B ILE* 3.8 30.3 - - + -
239B TRP* 3.4 35.4 - + + -
240B PRO 3.8 11.2 - - - +
241B ALA* 3.7 18.4 - - + -
261B VAL* 3.9 18.1 - - + +
262B GLN* 1.3 72.6 - - - +
264B PHE* 1.4 62.2 + - - +
265B GLY 3.7 0.2 + - - -
266B ASP* 3.4 13.7 - - - +
267B GLY* 2.9 31.4 + - - -
268B LYS 2.9 33.2 + - - -
270B SER* 2.8 32.0 + - - +
272B VAL* 4.1 2.7 - - + -
356B BTB 3.4 36.3 - - - -
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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
------------------------------------------------------------
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