Contacts of the helix formed by residues 255 - 270 (chain B) in PDB entry 4M5X
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 SER 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B ASP* 2.6 34.2 + - - -
251B ASP 3.0 14.9 + - - -
252B SER 4.5 4.0 - - - +
253B SER 3.7 1.0 - - - -
254B LYS* 1.3 76.4 - - - +
256B VAL* 1.3 55.7 + - - +
257B PRO* 3.2 7.5 - - - +
258B LEU* 2.9 27.8 + - - +
259B ALA* 2.9 29.1 + - - +
282B SER* 3.8 4.2 - - - -
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LYS 3.3 3.5 + - - +
255B SER* 1.3 68.5 - - - +
257B PRO* 1.3 75.1 - - + +
259B ALA* 3.1 1.9 + - - +
260B LEU* 2.9 25.0 + - + +
279B LEU* 4.7 3.1 - - + -
282B SER* 3.5 28.9 - - - +
283B PHE* 3.7 25.8 - - + -
303B LEU* 4.3 26.5 - - + +
306B ASN* 3.6 37.9 + - + +
307B VAL* 5.6 1.6 - - + -
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Residues in contact with PRO 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B MET* 3.4 28.2 - - + +
247B THR* 4.1 4.7 - - + -
250B ASP* 4.5 0.7 - - - +
255B SER* 3.2 13.0 - - - +
256B VAL* 1.3 95.2 - - + +
258B LEU* 1.3 61.3 + - - +
260B LEU* 3.3 1.4 + - + +
261B GLN* 3.1 26.3 + - - +
306B ASN* 4.1 18.4 - - - +
307B VAL* 4.7 6.5 - - + -
310B LYS* 3.8 35.0 - - + -
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Residues in contact with LEU 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B THR* 3.9 16.2 - - - +
250B ASP* 4.5 4.3 - - + +
252B SER* 3.7 14.8 - - - +
255B SER* 2.9 22.3 + - - +
257B PRO* 1.3 76.4 - - - +
259B ALA* 1.3 62.6 + - - +
261B GLN* 3.2 24.6 + - + +
262B ARG* 3.0 47.0 + - - +
540B LEU* 4.4 10.1 - - + -
543B ARG* 3.5 48.9 - - - +
544B LEU* 4.9 7.6 - - + -
547B GLU* 4.5 0.4 - - - +
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Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B SER 5.8 1.1 - - - +
255B SER 2.9 18.3 + - - +
256B VAL 3.1 3.6 + - - +
258B LEU* 1.3 76.6 - - - +
260B LEU* 1.3 57.7 + - - +
262B ARG* 3.3 23.0 + - - +
263B VAL* 3.2 31.5 + - - +
278B LYS 4.0 3.4 - - - +
279B LEU* 3.7 23.2 + - + +
282B SER* 3.6 18.6 - - - +
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 4.0 23.3 - - + -
232B LEU* 5.5 6.3 - - + -
238B LEU* 6.0 2.2 - - + -
242B VAL* 4.2 13.9 - - + -
256B VAL* 2.9 18.1 + - + +
257B PRO* 3.8 5.8 - - + +
259B ALA* 1.3 74.3 - - - +
261B GLN* 1.3 60.0 + - - +
263B VAL* 3.4 3.9 + - + +
264B PHE* 3.0 65.4 + - + -
279B LEU* 4.3 12.3 - - + +
303B LEU* 4.9 19.5 - - + -
304B LEU* 6.4 1.8 - - + -
307B VAL* 3.8 26.5 - - + -
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Residues in contact with GLN 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B VAL* 3.1 37.1 + - + +
243B TYR* 3.7 16.1 + - - -
245B MET* 3.1 29.2 + - + +
247B THR* 2.5 35.4 + - - +
257B PRO 3.1 13.4 + - - +
258B LEU* 3.2 17.7 + - + +
260B LEU* 1.3 77.0 - - - +
262B ARG* 1.3 55.0 + - - +
264B PHE* 3.8 2.2 - - - +
265B TYR* 2.9 32.7 + - - +
540B LEU* 3.6 26.5 - - + +
544B LEU* 4.2 2.0 - - - +
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Residues in contact with ARG 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B SER* 3.1 21.4 + - - -
258B LEU* 3.0 25.1 + - - +
259B ALA* 3.3 40.3 + - - +
260B LEU 3.3 0.2 - - - -
261B GLN* 1.3 76.7 - - - +
263B VAL* 1.3 61.2 + - + +
265B TYR* 3.3 3.0 + - + +
266B GLU* 2.9 43.8 + - + +
278B LYS* 3.3 39.3 - - - +
279B LEU 5.2 0.2 - - - +
544B LEU* 3.9 23.4 - - + +
547B GLU* 2.7 39.5 + - - +
551B GLU* 5.9 0.4 - - - -
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 4.2 15.7 - - + -
229B LEU* 4.5 14.1 - - + -
259B ALA 3.2 15.7 + - - +
260B LEU* 3.9 6.3 - - + +
261B GLN 3.4 0.2 - - - -
262B ARG* 1.3 78.0 - - + +
264B PHE* 1.3 67.5 + - + +
266B GLU* 3.2 2.3 + - - +
267B LEU* 2.8 46.6 + - + +
274B VAL* 4.3 6.5 - - + +
275B GLY 4.0 19.7 - - - +
276B THR* 4.5 3.6 - - + -
279B LEU* 4.3 23.1 - - + -
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Residues in contact with PHE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 4.0 8.7 - - + -
232B LEU* 3.9 15.3 - - + -
233B PHE* 3.3 50.9 - + + -
238B LEU* 5.0 3.4 - - + -
239B ARG* 3.7 33.4 - - + -
242B VAL* 3.8 31.4 - - + -
243B TYR* 3.2 25.5 + + + +
260B LEU* 3.0 40.7 + - + +
261B GLN* 3.9 0.4 - - - +
263B VAL* 1.3 82.9 - - + +
265B TYR* 1.3 63.5 + - - +
267B LEU* 3.2 1.4 + - + -
268B GLN 2.9 18.5 + - - -
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Residues in contact with TYR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B TYR* 3.6 11.8 + - + -
261B GLN 2.9 19.0 + - - +
262B ARG 3.5 3.6 - - - +
264B PHE* 1.3 77.4 - - - +
266B GLU* 1.3 80.4 + - + +
268B GLN 3.1 0.9 + - - -
269B HIS* 3.0 72.6 + + + +
536B ILE* 4.0 15.7 - - + -
540B LEU* 6.0 0.2 - - + -
541B VAL* 4.1 24.1 - - + +
544B LEU* 3.6 34.1 - - + -
545B GLN* 4.0 25.3 + - + +
548B LYS* 4.9 11.2 + - + -
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Residues in contact with GLU 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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214B VAL* 4.3 0.7 - - - +
262B ARG* 2.9 31.4 + - + +
263B VAL 3.9 2.0 - - - +
265B TYR* 1.3 86.5 - - + +
267B LEU* 1.3 61.7 + - - +
269B HIS* 5.6 0.7 - - - +
270B SER* 2.8 53.6 + - - +
274B VAL* 3.7 25.8 - - + +
544B LEU* 6.0 0.3 - - - +
548B LYS* 3.2 44.3 + - - +
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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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213B TYR* 5.9 0.3 - - - -
214B VAL* 3.7 47.4 + - + +
215B GLY 4.0 2.0 - - - +
216B LEU* 4.0 15.3 - - + -
229B LEU 4.6 4.9 - - - +
230B GLN* 3.9 20.6 - - - +
233B PHE* 3.7 45.8 - - + -
263B VAL* 2.8 38.0 + - + +
264B PHE* 3.7 5.4 - - + +
266B GLU* 1.3 77.8 - - - +
268B GLN* 1.3 59.9 + - - +
270B SER 4.7 1.4 + - - +
274B VAL* 3.9 11.2 - - + -
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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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233B PHE* 3.8 8.0 - - + -
239B ARG* 3.0 30.2 + - - +
243B TYR* 2.7 28.6 + - - +
264B PHE 2.9 15.3 + - - +
265B TYR 3.6 4.3 - - - +
267B LEU* 1.3 80.2 - - - +
269B HIS* 1.3 65.1 + - + +
531B VAL* 3.7 7.2 + - - +
532B THR* 3.5 24.2 + - - +
533B ASP* 3.3 26.1 + - - +
536B ILE* 3.7 14.2 - - - +
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Residues in contact with HIS 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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209B LYS* 5.5 0.5 + - - -
265B TYR* 3.0 61.9 + + + +
266B GLU* 5.0 1.6 - - - +
268B GLN* 1.3 88.2 + - + +
270B SER* 1.3 66.1 + - - +
271B ASP* 3.8 6.1 + - - +
533B ASP* 3.2 41.5 + - + -
536B ILE* 3.4 23.0 - - + +
548B LYS* 6.3 0.7 - - - +
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LYS* 3.9 7.4 + - - -
214B VAL* 3.7 18.0 - - - +
266B GLU* 2.8 43.4 + - - -
267B LEU 4.9 1.2 - - - +
269B HIS* 1.3 76.0 - - - +
271B ASP* 1.3 59.5 + - - +
272B LYS* 2.8 33.8 + - - +
273B PRO 4.9 0.3 + - - -
274B VAL* 4.4 4.4 - - - +
548B LYS* 5.7 1.8 - - - +
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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