Contacts of the helix formed by residues 256 - 270 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B GLN* 5.7 1.8 + - - -
230B TRP* 3.1 41.0 + - + +
254B ALA* 3.2 6.1 - - - +
255B MSE 1.3 79.0 - - - +
257B ASP* 1.3 64.8 + - - +
258B ASP* 3.3 12.8 + - - +
259B LEU* 2.8 39.8 + - - +
260B ALA* 3.1 18.5 + - - +
283B PHE 3.1 13.2 - - - +
284B ASP* 3.4 22.8 + - - +
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Residues in contact with ASP 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ASN* 1.3 72.2 - - - +
258B ASP* 1.3 61.2 + - - +
260B ALA* 3.1 2.1 + - - +
261B LEU* 2.8 35.5 + - + +
282B GLY* 3.5 4.9 - - - -
283B PHE 2.9 23.2 + - - +
284B ASP* 4.3 1.0 + - - -
285B ASP* 3.1 11.6 + - - -
286B VAL* 2.9 52.8 + - + +
289B GLY* 5.5 0.3 - - - -
296B LEU* 3.8 17.8 - - + +
298B THR* 2.7 26.2 + - - +
340B ARG* 5.5 1.0 + - - -
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Residues in contact with ASP 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ASP* 5.8 0.2 - - - -
80B GLN* 4.8 12.0 - - - +
81B ALA* 4.5 16.7 + - - +
82B PHE* 5.3 2.4 + - - +
230B TRP 4.1 3.8 - - - +
231B ASP* 4.0 9.0 - - - +
232B ARG* 2.8 69.9 + - + +
256B ASN* 3.3 15.3 + - - +
257B ASP* 1.3 77.9 - - - +
259B LEU* 1.3 61.7 + - - +
261B LEU* 3.3 1.8 + - - +
262B GLY 3.1 18.5 + - - -
284B ASP* 5.6 0.2 + - - -
286B VAL* 4.9 6.3 - - - +
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Residues in contact with LEU 259 (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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190B LEU* 3.8 25.4 - - + +
191B GLY* 4.2 4.3 - - - -
227B VAL* 3.9 13.2 - - + -
229B THR 3.9 15.7 - - - +
230B TRP* 3.8 31.4 - - + -
231B ASP 3.5 19.0 + - - +
235B GLY* 3.6 23.1 - - - +
254B ALA* 4.0 7.9 - - + -
255B MSE 3.9 11.9 - - + +
256B ASN* 2.8 25.0 + - - +
258B ASP* 1.3 72.8 - - - +
260B ALA* 1.3 57.5 + - - +
262B GLY 3.4 0.3 + - - -
263B ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ALA* 3.6 20.3 - - + +
256B ASN 3.1 10.4 + - - +
257B ASP 3.1 6.5 + - - +
259B LEU* 1.3 76.7 - - - +
261B LEU* 1.3 58.4 + - - +
263B ALA* 3.3 6.8 + - - +
264B LEU* 2.9 29.6 + - - +
280B LEU* 3.6 9.7 - - + +
281B MSE 4.0 2.9 - - - +
282B GLY* 4.0 8.1 - - - -
296B LEU* 4.0 28.0 - - + -
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Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TYR* 4.0 11.4 - - + +
232B ARG* 3.6 44.2 - - - +
257B ASP* 2.8 27.4 + - + +
258B ASP 3.3 4.2 + - - +
260B ALA* 1.3 70.3 - - - +
262B GLY* 1.3 64.5 + - - +
264B LEU* 3.3 11.2 + - + +
265B ARG 3.3 15.9 + - - -
286B VAL* 4.3 9.2 - - + -
288B ASP* 4.1 12.8 - - + +
289B GLY* 4.6 6.5 - - - +
292B THR* 3.6 33.0 - - + +
296B LEU* 4.2 17.5 - - + -
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Residues in contact with GLY 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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291A TYR* 4.8 7.0 - - - -
232B ARG* 3.4 29.5 - - - +
236B ALA* 3.3 22.3 - - - +
258B ASP 3.1 11.1 + - - -
259B LEU 3.8 1.3 - - - -
261B LEU* 1.3 75.7 - - - +
263B ALA* 1.3 62.1 + - - +
265B ARG* 3.2 11.1 + - - +
266B SER 3.3 8.7 + - - -
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Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU* 3.9 14.8 - - + -
235B GLY 3.8 2.2 - - - -
239B MSE 3.8 34.2 - - + +
259B LEU 2.9 18.4 + - - +
260B ALA* 3.3 8.0 + - - +
262B GLY* 1.3 75.8 - - - +
264B LEU* 1.3 62.9 + - - +
266B SER* 3.1 3.8 + - - -
267B LEU* 3.0 27.7 + - + +
280B LEU* 4.5 11.0 - - + -
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Residues in contact with LEU 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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260B ALA 2.9 16.3 + - - +
261B LEU* 3.6 12.8 - - + +
262B GLY 3.2 0.4 - - - -
263B ALA* 1.3 77.6 - - - +
265B ARG* 1.3 57.1 + - - +
267B LEU* 3.3 4.0 + - - +
268B GLN* 2.9 63.7 + - + +
274B VAL* 4.0 28.9 - - + -
280B LEU* 3.7 22.2 - - + +
292B THR* 4.0 33.2 - - + +
294B PRO* 4.2 13.7 - - + +
296B LEU* 5.9 3.6 - - + -
342B SER* 6.0 0.2 - - - -
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Residues in contact with ARG 265 (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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290A ARG 3.7 10.1 + - - -
291A TYR* 3.5 40.5 - - - +
292A THR 2.8 33.6 + - - +
293A TYR* 3.8 14.0 - - + -
295A SER* 3.5 6.8 + - - +
341A GLU* 2.9 42.4 + - - -
236B ALA* 5.3 2.7 - - + -
261B LEU 3.3 3.2 + - - +
262B GLY* 3.2 11.4 + - - +
264B LEU* 1.3 76.7 - - - +
266B SER* 1.3 60.3 + - - +
268B GLN* 3.2 11.2 + - - +
269B GLU* 2.9 55.6 + - - +
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Residues in contact with SER 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ALA* 2.7 39.0 + - - +
239B MSE 3.9 7.9 - - - -
240B ALA* 3.8 15.9 + - - +
243B LEU* 4.0 3.1 - - - -
262B GLY 3.3 1.2 + - - -
263B ALA 3.1 8.5 + - - -
265B ARG* 1.3 78.8 - - - +
267B LEU* 1.3 61.1 + - - +
269B GLU* 3.5 11.4 + - - +
270B ARG* 2.9 41.4 + - - +
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Residues in contact with LEU 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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239B MSE 4.2 15.7 - - + -
243B LEU* 3.9 26.9 - - + -
249B MSE 5.2 0.9 - - - -
252B VAL* 5.2 0.2 - - + -
263B ALA* 3.0 24.3 + - + +
264B LEU* 3.6 8.5 - - - +
266B SER* 1.3 77.4 - - - +
268B GLN* 1.3 63.2 + - - +
270B ARG* 3.2 8.0 + - - +
272B VAL* 3.0 51.9 + - + +
274B VAL* 4.1 26.2 - - + -
278B VAL* 4.1 24.2 - - + -
280B LEU* 4.5 12.8 - - + -
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Residues in contact with GLN 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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268A GLN* 5.9 1.4 + - - +
293A TYR* 3.2 53.8 + - + +
264B LEU* 2.9 51.3 + - + +
265B ARG* 3.9 2.5 - - - +
267B LEU* 1.3 77.7 - - + +
269B GLU* 1.3 64.0 + - - +
270B ARG 3.1 0.2 - - - -
271B GLY* 3.0 14.7 + - - +
272B VAL 4.5 9.2 - - - +
274B VAL* 5.4 1.8 - - + -
293B TYR 3.0 28.3 + - - +
294B PRO* 4.0 4.0 - - + +
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Residues in contact with GLU 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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293A TYR* 3.7 23.8 + - + -
341A GLU* 5.0 0.5 - - - +
240B ALA* 5.0 1.6 - - - +
265B ARG* 2.9 49.8 + - - +
266B SER* 3.5 10.0 + - - +
268B GLN* 1.3 78.2 - - - +
270B ARG* 1.3 94.1 + - + +
271B GLY 3.5 0.2 - - - -
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Residues in contact with ARG 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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240B ALA* 3.5 21.2 - - - +
243B LEU* 3.8 23.5 - - - +
244B ASP* 2.9 42.7 + - - +
266B SER* 2.9 31.9 + - - +
267B LEU 3.2 4.4 + - - +
268B GLN 3.1 0.6 - - - -
269B GLU* 1.3 111.5 + - + +
271B GLY* 1.3 59.8 + - - +
272B VAL* 3.2 13.5 + - + +
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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