Contacts of the helix formed by residues 262 - 274 (chain B) in PDB entry 6KJV
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 GLU 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372A ASP 5.5 4.9 - - - -
380A ARG* 5.1 4.7 - - - +
261B SER* 1.3 84.0 + - - +
263B GLN* 1.3 64.4 + - - +
264B TRP* 3.3 41.5 + - + +
265B ILE* 3.4 26.0 + - + +
266B PHE* 4.2 2.3 + - - +
1160B TYR 3.9 4.0 + - - +
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Residues in contact with GLN 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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370A VAL* 5.4 9.3 - - + +
261B SER 3.9 1.8 + - - -
262B GLU* 1.3 70.7 - - - +
264B TRP* 1.3 65.6 + - - +
265B ILE 3.2 0.6 + - - -
266B PHE* 3.6 15.6 + - - +
267B ARG* 3.8 13.9 + - - +
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Residues in contact with TRP 264 (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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367A PHE* 3.4 40.9 - + + -
370A VAL* 5.1 8.2 - - + +
372A ASP* 5.2 13.5 - - - -
380A ARG* 3.8 29.2 - - + -
383A LYS* 6.4 0.4 - - + -
384A LEU* 3.4 37.0 - - + +
262B GLU* 3.4 37.4 + - + +
263B GLN* 1.3 75.5 - - - +
265B ILE* 1.3 88.0 + - + +
266B PHE 3.3 0.2 - - - -
267B ARG* 3.2 4.1 + - - -
268B LEU* 3.0 42.8 + - + -
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Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ARG* 5.3 4.0 - - + -
261B SER* 5.0 4.7 - - - +
262B GLU* 3.5 26.2 - - + +
263B GLN 3.2 0.6 - - - -
264B TRP* 1.3 121.5 - - + +
266B PHE* 1.3 56.3 + - - +
268B LEU* 3.0 9.7 + - + +
269B TYR* 2.9 60.8 + - + +
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Residues in contact with PHE 266 (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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175B THR* 4.2 16.2 - - + -
178B TYR* 3.6 37.5 - + + -
179B ILE* 4.0 18.6 - - + -
182B ASN* 4.4 14.6 - - - -
243B TRP* 5.4 2.5 - + - -
262B GLU 4.2 1.5 + - - +
263B GLN* 3.6 12.6 + - - +
264B TRP 3.3 0.4 - - - -
265B ILE* 1.3 77.7 - - - +
267B ARG* 1.3 65.6 + - + +
269B TYR* 3.2 21.1 + + + +
270B VAL* 3.0 41.5 + - + +
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Residues in contact with ARG 267 (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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365A VAL 4.6 0.2 + - - -
366A ILE* 2.8 46.8 + - + +
367A PHE* 4.0 18.4 - - + -
368A ALA* 3.3 21.2 - - - +
369A PHE* 4.2 24.1 - - - +
370A VAL* 5.3 5.8 - - + +
263B GLN 3.9 13.4 + - - +
264B TRP* 3.2 9.5 + - - +
266B PHE* 1.3 82.2 - - - +
268B LEU* 1.3 58.7 + - - +
270B VAL* 3.0 18.2 - - + +
271B ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 268 (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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366A ILE* 5.6 2.7 - - + -
367A PHE* 4.7 15.2 - - + -
264B TRP* 3.0 35.9 + - + +
265B ILE* 3.0 15.2 + - + +
267B ARG* 1.3 75.6 - - - +
269B TYR* 1.3 68.7 + - + +
271B ALA* 3.1 12.7 + - + +
272B ILE* 3.0 38.3 + - + +
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Residues in contact with TYR 269 (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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179B ILE* 4.1 28.0 - - + -
243B TRP* 3.9 19.5 - - + -
246B VAL* 4.0 25.9 - - + +
249B VAL* 4.6 19.2 - - + +
250B TYR* 4.1 28.5 + + + -
253B THR* 4.3 9.0 + - - +
265B ILE* 2.9 44.9 + - + +
266B PHE* 3.2 20.6 + + + +
268B LEU* 1.3 80.4 - - + +
270B VAL* 1.3 57.8 + - + +
272B ILE* 3.0 9.1 + - + +
273B GLY* 2.9 27.0 + - - -
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Residues in contact with VAL 270 (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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366A ILE* 5.6 2.5 - - + +
182B ASN* 4.4 5.8 - - - +
243B TRP* 3.6 27.8 - - + -
266B PHE* 3.0 33.7 + - + +
267B ARG* 3.0 38.4 - - + +
269B TYR* 1.3 76.2 - - - +
271B ALA* 1.3 61.2 + - + +
274B TRP* 3.3 27.4 + - + +
275B GLY 3.6 3.6 + - - -
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Residues in contact with ALA 271 (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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366A ILE* 3.9 31.6 - - + -
267B ARG 2.9 17.1 + - - +
268B LEU* 3.1 15.8 + - + +
270B VAL* 1.3 79.2 - - + +
272B ILE* 1.3 57.7 + - + +
275B GLY* 3.2 25.4 - - - +
276B VAL* 3.2 9.2 + - - +
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Residues in contact with ILE 272 (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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242B TYR* 3.6 27.1 - - + +
245B LEU* 4.7 10.3 - - + -
246B VAL* 3.7 24.5 - - + -
249B VAL* 6.1 5.2 - - + -
268B LEU* 3.0 33.0 + - + +
269B TYR* 3.0 11.6 + - + +
271B ALA* 1.3 78.8 - - + +
273B GLY* 1.3 65.0 + - - +
276B VAL* 3.5 16.2 + - + +
277B PRO* 3.2 19.4 - - - +
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Residues in contact with GLY 273 (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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239B ALA* 3.5 15.8 - - - +
242B TYR* 4.0 10.9 - - - +
243B TRP* 3.3 37.7 - - - -
246B VAL* 4.4 0.6 - - - +
269B TYR 2.9 14.3 + - - -
272B ILE* 1.3 73.7 - - - +
274B TRP* 1.3 57.0 + - - +
277B PRO* 3.2 19.6 - - - +
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Residues in contact with TRP 274 (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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182B ASN* 3.2 37.9 + - - -
185B ALA* 4.2 12.6 - - + -
186B SER* 3.8 25.8 - - - -
189B LEU* 4.8 15.0 - - + -
235B TYR* 2.5 61.5 + + - +
236B CYS* 5.8 1.6 - - - -
239B ALA* 4.0 19.1 - - + -
243B TRP* 3.1 32.7 - + - +
270B VAL* 3.3 18.4 + - + +
273B GLY* 1.3 75.7 - - - +
275B GLY* 1.3 63.9 + - - +
276B VAL 3.8 0.4 - - - -
277B PRO* 3.9 1.8 - - - -
278B LEU* 4.0 5.7 + - - +
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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