Contacts of the helix formed by residues 262 - 274 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A SER* 1.3 84.1 + - - +
263A GLN* 1.3 63.7 + - - +
264A TRP* 3.3 40.7 + - + +
265A ILE* 3.4 25.1 + - + +
266A PHE* 4.3 1.9 + - - +
1160A TYR 3.9 3.1 + - - +
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Residues in contact with GLN 263 (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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261A SER 3.9 3.1 + - - +
262A GLU* 1.3 70.7 - - - +
264A TRP* 1.3 64.4 + - - +
265A ILE 3.2 1.1 + - - -
266A PHE* 3.6 15.3 + - - +
267A ARG* 3.7 14.6 + - - +
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Residues in contact with TRP 264 (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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262A GLU* 3.4 42.1 + - + +
263A GLN* 1.3 77.1 - - - +
265A ILE* 1.3 87.2 + - + +
267A ARG* 3.2 11.8 + - + +
268A LEU* 3.0 46.4 + - + +
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Residues in contact with ILE 265 (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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261A SER* 5.1 4.5 - - - +
262A GLU* 3.5 30.3 - - + +
263A GLN 3.2 0.8 - - - -
264A TRP* 1.3 113.2 - - + +
266A PHE* 1.3 57.6 - - - +
268A LEU* 3.0 10.1 + - + +
269A TYR* 2.9 59.4 + - + +
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Residues in contact with PHE 266 (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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175A THR* 4.2 18.6 - - + -
178A TYR* 3.8 29.6 - + + -
179A ILE* 3.8 24.2 - - + -
182A ASN* 4.5 14.1 - - - -
243A TRP* 5.4 2.0 - + - -
262A GLU 4.3 1.0 + - - +
263A GLN* 3.6 13.2 + - - +
264A TRP 3.3 0.6 - - - -
265A ILE* 1.3 78.8 - - - +
267A ARG* 1.3 63.8 + - + +
269A TYR* 3.2 21.3 + + + +
270A VAL* 3.0 42.4 + - + +
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Residues in contact with ARG 267 (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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263A GLN 3.7 15.6 + - - +
264A TRP* 3.2 13.2 + - + +
266A PHE* 1.3 82.1 - - - +
268A LEU* 1.3 60.7 + - - +
270A VAL* 3.0 18.8 - - + +
271A ALA* 2.9 27.2 + - - +
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Residues in contact with LEU 268 (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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264A TRP* 3.0 36.6 + - + +
265A ILE* 3.0 13.2 + - + +
267A ARG* 1.3 74.8 - - - +
269A TYR* 1.3 69.1 + - + +
271A ALA* 3.2 13.2 + - + +
272A ILE* 2.9 37.7 + - + +
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Residues in contact with TYR 269 (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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179A ILE* 4.2 26.9 - - + -
243A TRP* 4.0 13.3 - - + -
246A VAL* 3.9 30.0 - - + +
249A VAL* 4.4 21.2 - - + +
250A TYR* 4.1 27.6 + + + -
253A THR* 4.2 10.4 + - - +
265A ILE* 2.9 44.2 + - + +
266A PHE* 3.2 22.0 + + + +
268A LEU* 1.3 79.5 - - + +
270A VAL* 1.3 58.1 + - - +
272A ILE* 3.0 9.3 + - + +
273A GLY* 2.9 26.9 + - - -
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Residues in contact with VAL 270 (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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182A ASN* 4.6 5.2 - - - +
243A TRP* 3.6 28.3 - - + -
266A PHE* 3.0 36.7 + - + +
267A ARG* 3.0 39.9 - - + +
269A TYR* 1.3 76.8 - - - +
271A ALA* 1.3 60.6 + - + +
274A TRP* 3.3 28.3 + - + +
275A GLY 3.6 3.5 + - - -
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Residues in contact with ALA 271 (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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267A ARG 2.9 17.8 + - - +
268A LEU* 3.6 19.1 - - + +
269A TYR 3.2 0.2 - - - -
270A VAL* 1.3 80.1 - - - +
272A ILE* 1.3 57.5 + - + +
275A GLY* 3.1 9.3 - - - +
276A VAL* 3.1 26.3 + - - +
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Residues in contact with ILE 272 (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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242A TYR* 3.6 28.0 - - + +
245A LEU* 4.7 10.5 - - + -
246A VAL* 3.7 23.1 - - + -
249A VAL* 6.3 3.4 - - + -
268A LEU* 2.9 29.7 + - + +
269A TYR* 3.0 12.3 + - + +
271A ALA* 1.3 78.0 - - + +
273A GLY* 1.3 66.8 + - - +
276A VAL* 3.5 17.7 + - + +
277A PRO* 3.2 19.6 - - - +
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Residues in contact with GLY 273 (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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239A ALA* 3.6 15.9 - - - +
242A TYR* 3.9 11.2 - - - +
243A TRP* 3.3 37.3 - - - -
246A VAL* 4.4 0.6 - - - +
269A TYR 2.9 14.3 + - - -
272A ILE* 1.3 74.5 - - - +
274A TRP* 1.3 57.2 + - - +
277A PRO* 3.2 19.4 - - - +
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Residues in contact with TRP 274 (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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182A ASN* 3.1 39.9 + - - -
185A ALA* 4.3 13.0 - - + -
186A SER* 3.9 26.5 - - - -
189A LEU* 4.8 14.6 - - + -
235A TYR* 2.4 61.6 + + - +
236A CYS* 5.8 1.1 - - - -
239A ALA* 3.9 20.4 - - + -
243A TRP* 3.1 29.9 - + - +
270A VAL* 3.3 17.7 + - + +
273A GLY* 1.3 75.2 - - - +
275A GLY* 1.3 64.9 + - - +
276A VAL 3.7 0.4 - - - -
277A PRO* 3.9 1.6 - - - -
278A LEU* 4.0 4.7 + - - +
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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