Contacts of the helix formed by residues 261 - 275 (chain A) in PDB entry 1KYH
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 ALA 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.9 6.5 - - + -
211A LYS* 5.8 1.6 - - - +
212A GLY 4.2 6.6 + - - +
213A GLY* 3.3 41.3 - - - +
214A THR* 3.5 18.3 - - + +
217A THR* 3.5 14.7 - - + +
259A LEU* 4.2 1.0 + - - +
260A LEU* 1.3 71.3 - - - +
262A HIS* 1.3 63.1 + - - +
264A LEU* 3.0 26.3 + - - +
265A SER 4.1 0.2 + - - -
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Residues in contact with HIS 262 (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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45A LEU* 3.5 22.5 - - + +
48A LEU* 4.4 18.2 - - + +
217A THR* 4.6 2.2 - - - -
260A LEU* 3.8 31.7 - - + +
261A ALA* 1.3 78.0 - - - +
263A GLU* 1.3 80.2 + - + +
265A SER* 3.2 21.2 + - - +
266A ASP* 3.5 18.4 + - - +
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Residues in contact with GLU 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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250A TRP* 3.3 34.9 - - + -
258A THR 4.3 0.9 - - - +
259A LEU* 3.9 8.1 - - + -
260A LEU* 2.9 46.1 + - - +
262A HIS* 1.3 97.4 - - + +
264A LEU* 1.3 64.5 + - - +
266A ASP* 3.1 15.3 + - + +
267A ILE* 3.0 31.3 + - + +
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Residues in contact with LEU 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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209A LEU* 3.8 12.8 - - + -
214A THR* 4.1 13.7 - - + -
217A THR* 3.6 22.0 - - - +
221A MSE 3.8 13.0 - - + +
243A HIS* 3.7 23.3 - - + +
246A CYS* 3.5 21.0 - - + +
247A ALA* 3.6 28.7 - - - +
259A LEU* 3.8 24.9 - - + -
261A ALA* 3.0 13.8 + - - +
263A GLU* 1.3 77.6 - - - +
265A SER* 1.3 58.1 + - - +
267A ILE* 3.2 3.1 + - + -
268A LEU* 3.0 24.9 + - - +
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Residues in contact with SER 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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45A LEU 4.6 0.7 + - - -
48A LEU* 4.0 14.9 - - - +
49A GLY* 3.6 24.6 + - - -
52A ARG* 3.0 39.9 + - - +
217A THR* 4.5 10.6 - - - +
221A MSE 4.0 12.8 - - - +
262A HIS* 3.2 13.0 + - - -
263A GLU 3.1 0.4 - - - -
264A LEU* 1.3 80.5 - - - +
266A ASP* 1.3 61.2 + - - +
268A LEU* 3.7 0.7 + - - +
269A PRO* 3.3 10.6 - - - +
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Residues in contact with ASP 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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48A LEU* 6.0 2.3 - - - +
52A ARG* 4.4 15.8 + - - +
262A HIS* 3.7 22.7 + - - +
263A GLU* 3.1 26.2 + - + +
265A SER* 1.3 79.3 - - - +
267A ILE* 1.3 60.7 + - + +
269A PRO* 3.3 14.1 - - - +
270A ARG* 5.3 1.6 + - - +
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Residues in contact with ILE 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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246A CYS* 3.7 26.0 - - + +
249A LEU* 3.5 17.3 - - + -
250A TRP* 3.9 35.7 - - + -
259A LEU* 4.8 2.5 - - + -
263A GLU* 3.0 22.3 + - + +
264A LEU* 3.6 8.1 - - + +
265A SER 3.2 0.4 - - - -
266A ASP* 1.3 77.6 - - + +
268A LEU* 1.3 65.8 + - - +
269A PRO* 3.1 5.2 - - - -
270A ARG* 3.1 15.4 + - + +
271A VAL* 3.2 28.3 + - + -
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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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52A ARG* 3.9 22.2 - - + +
53A SER* 3.6 24.0 - - - +
221A MSE 3.9 18.8 - - + -
225A MSE 4.4 4.0 - - + -
242A LEU* 3.9 25.8 - - + -
246A CYS* 3.5 19.7 - - - -
264A LEU 3.0 15.2 + - - +
265A SER 3.9 4.5 - - - +
267A ILE* 1.3 75.4 - - - +
269A PRO* 1.3 69.7 - - + +
271A VAL* 4.3 1.3 - - + -
272A TRP* 2.8 50.1 + - + +
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Residues in contact with PRO 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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52A ARG* 3.6 35.7 - - - +
265A SER 3.3 13.2 - - - +
266A ASP 3.3 10.3 - - - +
267A ILE 3.2 5.4 - - - -
268A LEU* 1.3 94.1 - - + +
270A ARG* 1.3 63.4 + - + +
272A TRP* 4.0 3.9 - - + +
273A LYS* 3.4 19.2 + - - +
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A LEU* 4.9 11.4 - - + -
266A ASP 6.0 1.8 - - - +
267A ILE* 3.1 8.7 + - - +
269A PRO* 1.3 79.5 - - + +
271A VAL* 1.3 65.0 + - - +
273A LYS* 3.3 15.4 + - - +
274A ARG* 3.4 12.0 + - - +
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Residues in contact with VAL 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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242A LEU* 4.0 9.9 - - + -
245A ALA* 3.8 28.5 - - + +
246A CYS* 4.0 17.9 - - - -
249A LEU* 3.3 33.0 - - + -
267A ILE* 3.2 19.2 + - + +
268A LEU* 3.2 6.2 + - + +
270A ARG* 1.3 73.8 - - - +
272A TRP* 1.3 66.8 + - - +
274A ARG* 3.1 23.0 + - - +
275A PHE* 3.1 29.2 - - + -
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Residues in contact with TRP 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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15A LEU* 4.0 35.2 - - + +
16A PRO* 4.6 12.4 + - + -
52A ARG 4.0 5.2 - - - -
53A SER* 3.8 29.4 - - - -
54A GLY* 4.4 2.9 - - - -
225A MSE 3.6 40.2 - - + -
228A CYS* 4.2 12.8 - - - -
242A LEU* 4.3 13.2 - - + -
268A LEU* 2.8 42.6 + - + +
269A PRO* 4.0 4.7 - - + +
271A VAL* 1.3 73.5 - - - +
273A LYS* 1.3 63.5 + - - +
275A PHE* 2.9 13.9 + - - +
276A GLU* 3.4 34.1 + - + +
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Residues in contact with LYS 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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269A PRO 3.4 13.8 + - - +
270A ARG* 3.3 14.1 + - - +
272A TRP* 1.3 79.4 - - - +
274A ARG* 1.3 61.4 + - - +
276A GLU* 3.2 42.0 + - + +
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Residues in contact with ARG 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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8A GLU* 5.8 0.8 + - - -
12A ARG* 2.7 38.5 + - - +
245A ALA* 4.4 15.4 + - - +
248A GLU* 5.7 2.2 + - - +
249A LEU* 4.6 26.1 - - - +
270A ARG 3.4 7.6 + - - +
271A VAL* 3.1 18.7 + - - +
273A LYS* 1.3 79.2 - - - +
275A PHE* 1.3 85.2 + - - +
276A GLU 3.3 3.2 + - - +
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Residues in contact with PHE 275 (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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8A GLU* 3.8 33.2 - - + -
11A VAL* 3.9 15.5 - - + -
12A ARG* 3.4 36.8 + - + +
15A LEU* 3.6 25.3 - - + +
241A TYR* 3.5 37.0 - + - -
242A LEU* 3.7 14.1 - - + -
245A ALA* 4.5 1.3 - - + -
271A VAL* 3.1 33.4 - - + -
272A TRP 2.9 6.6 + - - +
274A ARG* 1.3 109.6 - - - +
276A GLU* 1.3 60.8 + - - +
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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