Contacts of the helix formed by residues 256 - 270 (chain A) in PDB entry 4KMR
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 ASN 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A PHE* 6.3 0.4 - - - +
230A TRP* 3.0 39.8 + - + +
254A ALA* 3.2 4.1 + - - +
255A MSE 1.3 77.1 - - - +
257A ASP* 1.3 65.5 + - - +
258A ASP* 3.7 12.9 + - - +
259A LEU* 2.8 40.1 + - - +
260A ALA* 3.1 20.6 + - - +
282A GLY* 4.0 0.3 - - - -
283A PHE 3.1 13.5 - - - +
284A ASP* 3.5 22.8 + - - +
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Residues in contact with ASP 257 (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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256A ASN* 1.3 70.9 - - - +
258A ASP* 1.3 61.1 + - - +
260A ALA* 3.1 7.9 + - - +
261A LEU* 2.9 33.9 + - - +
282A GLY* 3.5 3.1 - - - -
283A PHE 3.0 25.1 + - - +
284A ASP* 4.6 0.8 + - - -
285A ASP* 3.2 9.3 + - - +
286A VAL* 3.0 32.0 + - + -
287A ALA* 3.3 25.5 + - + +
289A GLY* 5.6 1.4 + - - -
296A LEU* 3.7 12.6 - - + +
298A THR* 2.7 27.7 + - - +
340A ARG* 5.8 0.2 + - - -
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Residues in contact with ASP 258 (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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80A GLN* 5.5 3.3 - - - +
81A ALA* 4.7 20.1 + - - +
82A PHE 5.4 1.0 + - - -
230A TRP 4.2 2.1 - - - +
231A ASP* 4.1 8.3 - - - -
232A ARG* 2.7 68.3 + - + +
256A ASN* 3.2 16.2 + - - +
257A ASP* 1.3 76.4 - - - +
259A LEU* 1.3 66.3 + - - +
261A LEU* 3.3 0.6 + - - +
262A GLY 3.1 18.5 + - - -
286A VAL* 5.3 6.5 - - - +
287A ALA* 5.4 1.2 - - - +
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Residues in contact with LEU 259 (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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190A LEU* 3.7 25.6 - - + +
191A GLY* 4.3 2.9 - - - -
227A VAL* 3.9 22.2 - - + -
230A TRP* 3.7 33.7 - - + +
231A ASP 3.5 24.2 + - - +
235A GLY* 3.6 23.1 - - - +
254A ALA* 3.9 10.1 - - + -
255A MSE 3.8 12.3 - - + +
256A ASN* 2.8 25.1 + - - +
258A ASP* 1.3 73.1 - - - +
260A ALA* 1.3 57.0 + - - +
262A GLY* 3.3 1.4 + - - -
263A ALA* 2.9 28.4 + - - +
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Residues in contact with ALA 260 (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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254A ALA* 3.6 16.3 - - + +
256A ASN 3.1 13.6 + - - +
257A ASP* 3.1 8.5 + - - +
259A LEU* 1.3 76.8 - - - +
261A LEU* 1.3 59.4 + - - +
263A ALA* 3.3 6.4 + - - +
264A LEU 2.8 23.0 + - - -
280A LEU* 3.5 13.7 - - + +
281A MSE 4.0 4.9 - - - +
282A GLY* 3.9 16.2 - - - -
296A LEU* 4.1 17.7 - - + -
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Residues in contact with LEU 261 (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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232A ARG* 3.3 32.1 - - - +
257A ASP 2.9 16.0 + - - +
258A ASP 4.1 2.2 - - - +
260A ALA* 1.3 74.3 - - - +
262A GLY* 1.3 64.9 + - - +
264A LEU* 3.4 25.2 + - + +
265A ARG* 3.2 20.6 + - - +
287A ALA* 3.5 29.2 - - + +
292A THR* 3.8 33.7 - - + +
296A LEU* 4.0 22.7 - - + -
291B TYR* 4.1 10.4 - - + +
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Residues in contact with GLY 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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232A ARG* 3.3 28.8 - - - +
236A ALA* 3.3 22.7 - - - +
258A ASP 3.1 10.7 + - - -
259A LEU 3.8 1.3 - - - -
261A LEU* 1.3 74.5 - - - +
263A ALA* 1.3 63.6 + - - +
265A ARG* 3.2 10.7 + - - +
266A SER 3.2 9.7 + - - -
291B TYR* 4.6 8.5 - - - -
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Residues in contact with ALA 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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190A LEU* 3.9 11.4 - - + -
235A GLY 3.9 1.2 - - - -
239A MSE 3.7 38.9 - - + +
259A LEU 2.9 14.7 + - - +
260A ALA* 3.3 11.2 + - - +
262A GLY* 1.3 77.2 - - - +
264A LEU* 1.3 62.0 - - - +
266A SER* 3.1 2.8 + - - -
267A LEU* 2.9 28.1 + - + +
280A LEU* 4.4 11.0 - - + -
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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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260A ALA 2.8 16.9 + - - +
261A LEU* 3.6 28.7 - - + +
262A GLY 3.2 0.2 - - - -
263A ALA* 1.3 76.1 - - - +
265A ARG* 1.3 57.2 + - - +
267A LEU* 3.2 4.5 + - - +
268A GLN* 2.8 59.0 + - - +
274A VAL* 3.9 23.1 - - + -
280A LEU* 3.7 20.8 - - + +
292A THR* 5.0 3.1 - - - -
293A TYR 3.9 17.7 - - - +
294A PRO* 4.0 19.7 - - + +
296A LEU* 5.8 1.1 - - + -
342A SER* 6.4 0.4 - - - -
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Residues in contact with ARG 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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236A ALA* 5.3 1.1 - - + -
261A LEU 3.2 4.1 + - - +
262A GLY 3.2 10.4 + - - +
264A LEU* 1.3 78.0 - - - +
266A SER* 1.3 58.9 + - - +
268A GLN* 3.2 9.5 + - - +
269A GLU* 2.9 53.9 + - - +
290B ARG 4.6 2.8 + - - -
291B TYR* 3.4 49.8 + - + +
292B THR 2.9 21.6 + - - +
293B TYR* 3.7 21.3 - - + -
295B SER* 3.8 7.9 - - - +
341B GLU* 2.8 41.6 + - - -
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Residues in contact with SER 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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236A ALA* 2.7 38.3 + - - +
239A MSE 4.0 5.8 - - - -
240A ALA* 3.7 19.1 - - - +
243A LEU* 4.4 1.1 - - - -
262A GLY 3.2 2.8 + - - -
263A ALA 3.1 8.1 + - - -
265A ARG* 1.3 77.9 - - - +
267A LEU* 1.3 62.0 + - - +
269A GLU* 3.4 13.1 + - - +
270A ARG* 3.1 39.3 + - - +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A MSE 4.2 19.7 - - + -
243A LEU* 3.8 24.7 - - + -
252A VAL* 5.1 0.2 - - + -
263A ALA* 2.9 24.8 + - + +
264A LEU* 3.5 9.2 - - - +
266A SER* 1.3 74.2 - - - +
268A GLN* 1.3 63.2 + - - +
270A ARG* 3.2 7.4 + - - -
271A GLY 3.3 0.2 + - - -
272A VAL* 3.0 54.7 + - + +
274A VAL* 4.0 25.8 - - + -
278A VAL* 4.2 23.3 - - + -
280A LEU* 4.5 13.2 - - + -
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Residues in contact with GLN 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 LEU* 2.8 38.5 + - + +
265A ARG* 3.9 2.7 - - - +
267A LEU* 1.3 77.6 - - + +
269A GLU* 1.3 59.8 + - - +
271A GLY* 3.0 19.4 + - - +
272A VAL 4.5 9.4 - - - +
274A VAL* 5.2 2.6 - - + +
293A TYR* 3.0 31.8 + - - +
294A PRO* 3.6 14.6 - - - +
268B GLN* 5.9 1.0 + - - +
293B TYR* 3.7 46.0 + - + +
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Residues in contact with GLU 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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240A ALA* 4.7 1.9 - - - +
265A ARG* 2.9 51.3 + - - +
266A SER* 3.4 11.2 + - - +
268A GLN* 1.3 78.3 - - - +
270A ARG* 1.3 94.7 + - + +
271A GLY 3.4 1.0 + - - -
293B TYR* 3.8 29.7 + - + -
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ALA* 3.3 27.5 + - - +
243A LEU* 3.7 23.1 - - - -
244A ASP* 2.9 41.1 + - - +
266A SER* 3.1 22.4 + - - +
267A LEU 3.2 5.2 + - - +
268A GLN 3.1 0.6 - - - -
269A GLU* 1.3 111.1 + - - +
271A GLY* 1.3 61.9 + - - +
272A VAL* 3.3 14.3 + - + +
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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
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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