Contacts of the helix formed by residues 256 - 277 (chain B) in PDB entry 3RAW
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 PRO 256 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B PRO 3.7 4.5 - - - +
255B TYR* 1.3 85.7 - - + +
257B LEU* 1.3 67.2 + - - +
258B PRO* 3.3 10.5 - - + -
259B HIS* 2.9 50.8 + - + +
260B VAL* 3.0 10.0 + - - +
308B GLU* 6.6 0.2 - - - -
309B LYS 5.8 3.1 - - - +
310B SER* 5.0 7.4 - - - +
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Residues in contact with LEU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B TYR 3.8 1.0 + - - -
256B PRO* 1.3 70.5 - - - +
258B PRO* 1.3 66.7 - - + +
260B VAL* 3.1 9.5 + - + +
261B ARG* 2.7 56.1 + - - +
368B TYR* 4.3 14.5 - - + -
441B GLU* 3.8 20.6 - - + +
442B HIS* 3.4 62.1 - - + +
445B LEU* 4.7 3.8 - - + -
471B PHE* 4.0 16.4 - - + -
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Residues in contact with PRO 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B PRO* 3.4 13.0 - - + -
257B LEU* 1.3 97.2 - - + +
259B HIS* 1.3 67.9 - - + +
261B ARG* 3.7 26.5 + - + +
262B HIS* 3.1 23.2 + - - +
441B GLU* 5.4 4.7 - - - +
479B GLU* 4.5 9.6 - - - +
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Residues in contact with HIS 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B TYR* 4.2 8.4 - - + -
256B PRO* 2.9 33.7 + - + +
258B PRO* 1.3 81.8 - - + +
260B VAL* 1.3 67.0 + - - +
262B HIS* 3.3 2.9 + - - +
263B MET* 2.9 40.4 + - + +
310B SER* 3.4 26.1 + - - -
311B VAL* 3.4 30.8 + - + +
314B THR* 3.4 26.6 - - + +
479B GLU* 6.1 0.7 - - - -
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B TYR* 3.5 26.7 - - + +
256B PRO 3.0 19.0 + - - +
257B LEU* 3.4 10.8 - - - +
259B HIS* 1.3 76.2 - - - +
261B ARG* 1.3 57.5 + - - +
263B MET* 3.3 7.7 + - - +
264B ALA* 2.9 28.9 + - - +
364B LEU* 4.2 25.9 - - + +
367B TYR* 3.9 22.2 - - + -
368B TYR* 4.0 7.2 - - + +
445B LEU* 4.5 26.0 - - + -
471B PHE* 5.0 2.2 - - + -
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Residues in contact with ARG 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 2.7 34.0 + - - +
258B PRO* 3.7 25.6 + - - +
259B HIS 3.1 0.2 - - - -
260B VAL* 1.3 74.3 - - - +
262B HIS* 1.3 63.2 + - - +
264B ALA* 3.5 2.6 + - - +
265B TYR* 3.1 22.9 + - - +
441B GLU* 3.3 31.9 + - - +
471B PHE* 3.0 53.5 + - + +
472B PHE* 3.6 5.3 - - + -
474B GLY* 3.3 41.0 + - - -
475B LEU* 3.7 15.8 - - + +
479B GLU* 5.3 2.4 + - - -
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Residues in contact with HIS 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PRO 3.1 15.1 + - - +
259B HIS 3.3 2.0 + - - +
261B ARG* 1.3 79.4 - - - +
263B MET* 1.3 61.8 + - - +
265B TYR* 3.5 2.7 + + - +
266B GLN* 2.8 56.8 + - + +
314B THR* 2.6 36.3 + - - +
315B SER 4.0 1.3 - - - -
475B LEU* 3.9 9.6 - - + +
479B GLU* 3.5 50.0 + - + +
482B PHE* 5.9 1.0 - - - -
484B THR* 3.6 32.1 + - + -
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Residues in contact with MET 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B THR* 4.5 4.3 - - - -
255B TYR* 3.8 27.8 - - + -
259B HIS* 2.9 44.8 + - + +
260B VAL* 3.8 6.7 - - - +
262B HIS* 1.3 72.9 - - - +
264B ALA* 1.3 65.8 + - - +
266B GLN* 3.3 5.9 + - - +
267B LEU* 3.0 25.0 + - - +
291B PHE* 3.8 24.0 - - - -
314B THR* 3.9 22.9 - - + +
316B ILE* 3.5 21.8 - - + +
367B TYR* 4.0 27.8 - - + -
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 2.9 18.3 + - + +
261B ARG* 3.5 8.1 - - - +
263B MET* 1.3 74.0 - - - +
265B TYR* 1.3 59.0 + - - +
267B LEU* 3.4 4.4 + - - +
268B CYS* 2.8 35.9 + - - -
360B ILE* 5.8 0.4 - - - -
364B LEU* 3.7 36.6 - - + +
471B PHE* 4.5 4.9 - - + -
472B PHE* 3.7 18.2 - - + -
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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
----------------------------------------------------------
261B ARG 3.1 14.5 + - - +
262B HIS* 3.6 6.5 - + - +
263B MET 3.3 0.2 - - - -
264B ALA* 1.3 80.1 - - - +
266B GLN* 1.3 61.3 + - + +
268B CYS* 3.4 2.8 + - - +
269B HIS* 2.9 29.8 + - + +
467B LEU* 3.9 27.0 - - + +
472B PHE* 3.8 25.4 - + + -
475B LEU* 3.5 31.6 - - + -
479B GLU 3.8 13.5 - - - -
480B ARG* 3.0 37.2 + - + +
482B PHE* 3.5 32.4 - + - -
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Residues in contact with GLN 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 3.6 26.6 - - + +
262B HIS* 2.8 49.9 + - + +
263B MET* 3.7 3.8 - - - +
264B ALA 3.3 0.4 - - - -
265B TYR* 1.3 79.2 - - + +
267B LEU* 1.3 60.9 + - - +
269B HIS* 3.4 4.0 + - - +
270B ALA* 2.9 30.9 + - - +
314B THR 3.0 23.8 + - - -
315B SER* 3.3 6.6 - - - -
316B ILE* 2.8 42.2 + - + +
317B ARG* 4.8 1.0 + - - -
318B VAL* 5.9 0.7 - - - -
482B PHE* 4.5 10.3 - - + -
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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
----------------------------------------------------------
263B MET 3.0 19.6 + - - +
264B ALA 3.7 3.1 - - - +
266B GLN* 1.3 73.4 - - - +
268B CYS* 1.3 65.9 + - - +
270B ALA* 4.5 3.1 - - - -
271B LEU* 2.9 37.0 + - + +
284B LEU* 4.9 5.8 - - + -
289B ILE* 3.4 43.5 - - + -
316B ILE* 4.2 6.7 - - + +
318B VAL* 4.1 17.9 - - + -
360B ILE* 4.4 30.5 - - + -
363B ILE* 4.2 16.6 - - + -
364B LEU* 4.4 9.6 - - + -
367B TYR* 4.4 6.5 - - + -
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Residues in contact with CYS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ALA* 2.8 31.0 + - - +
265B TYR* 3.8 1.3 - - - +
267B LEU* 1.3 72.8 - - - +
269B HIS* 1.3 57.3 + - - +
272B ARG* 2.9 32.9 + - - +
360B ILE* 4.6 6.5 - - - -
452B MET* 3.6 31.2 - - - -
463B LEU* 3.7 20.3 - - + +
466B ALA* 4.1 12.8 - - + -
467B LEU* 3.5 24.2 - - + -
472B PHE* 4.4 10.1 - - + -
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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
----------------------------------------------------------
216B LYS* 2.9 25.6 + - + -
217B PHE* 3.5 29.6 - + - -
218B LEU* 3.7 22.0 - - + -
265B TYR* 2.9 18.9 + - + +
266B GLN 3.5 3.6 - - - +
268B CYS* 1.3 74.4 - - - +
270B ALA* 1.3 66.9 + - - +
272B ARG* 3.9 6.2 + - - +
273B PHE* 3.4 18.7 + - - +
467B LEU* 3.7 18.8 - - + +
482B PHE* 3.3 43.4 - + + -
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B PHE* 3.3 27.5 - - - +
218B LEU* 4.3 5.4 - - + -
219B CYS* 4.9 3.1 - - - -
266B GLN 2.9 20.4 + - - +
267B LEU 3.9 1.8 - - - +
269B HIS* 1.3 72.6 - - - +
271B LEU* 1.3 66.1 + - + +
273B PHE* 3.2 19.9 + - - +
274B LEU* 3.4 12.3 + - - +
318B VAL* 3.7 29.6 - - + -
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Residues in contact with LEU 271 (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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267B LEU* 2.9 21.0 + - + +
270B ALA* 1.3 80.1 - - + +
272B ARG* 1.3 65.1 + - - +
274B LEU* 3.1 23.2 + - + +
275B HIS* 2.9 34.9 + - + +
281B HIS* 3.9 9.4 - - + -
284B LEU* 3.8 36.3 - - + -
318B VAL* 4.0 22.4 - - + -
356B ASP* 3.7 22.9 - - - +
360B ILE* 4.2 4.7 - - + -
463B LEU* 3.1 24.0 - - + -
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Residues in contact with ARG 272 (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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217B PHE* 3.4 34.8 - - - -
268B CYS 2.9 20.9 + - - +
269B HIS* 3.9 6.6 + - - +
270B ALA 3.3 0.2 - - - -
271B LEU* 1.3 75.4 - - - +
273B PHE* 1.3 78.0 + - - +
275B HIS* 3.4 6.5 + - + +
276B GLU* 3.0 49.9 + - + +
463B LEU* 3.5 12.5 - - + +
464B ALA* 4.0 29.6 - - + +
467B LEU* 4.3 20.9 - - + +
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Residues in contact with PHE 273 (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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208B ILE* 4.2 16.2 - - + -
211B LYS* 4.1 23.6 - - + -
212B ASP* 3.6 27.1 - - + -
217B PHE* 3.3 59.0 - + + -
219B CYS* 5.0 1.6 - - - -
269B HIS 3.4 2.9 + - - +
270B ALA 3.2 9.1 + - - +
272B ARG* 1.3 94.3 - - - +
274B LEU* 1.3 91.0 + - + +
276B GLU* 3.4 1.0 + - - +
277B ASN* 2.9 49.5 + - + +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 4.1 22.2 - - + -
219B CYS* 4.2 8.7 - - - -
270B ALA 3.6 10.8 - - - +
271B LEU* 3.1 30.7 + - + +
273B PHE* 1.3 105.3 - - + +
275B HIS* 1.3 60.6 + - + +
277B ASN* 3.0 21.1 + - + +
279B LEU* 3.1 42.9 + - + +
281B HIS* 5.0 5.8 - - + +
318B VAL* 5.7 0.2 - - + -
321B PHE* 3.7 29.2 - - + -
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Residues in contact with HIS 275 (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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271B LEU* 2.9 20.9 + - + +
272B ARG* 3.6 7.2 - - + +
274B LEU* 1.3 80.3 - - + +
276B GLU* 1.3 59.4 + - - +
277B ASN 3.1 0.2 - - - -
278B GLN* 3.3 13.2 + - - +
279B LEU 3.2 19.3 - - - -
280B THR* 4.5 0.2 - - - -
353B GLN* 3.4 48.2 + - + +
356B ASP* 2.8 34.9 + - + +
357B VAL* 4.4 4.2 - - + +
463B LEU* 3.7 32.0 + - + +
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ARG* 3.0 37.0 + - + +
273B PHE 3.9 4.7 - - - +
274B LEU 3.3 0.2 - - - -
275B HIS* 1.3 74.8 - - - +
277B ASN* 1.3 63.6 + - - +
278B GLN* 2.9 15.5 - - - +
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Residues in contact with ASN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LYS* 4.3 19.9 - - + +
273B PHE* 2.9 48.4 + - + +
274B LEU* 3.0 14.6 + - + +
276B GLU* 1.3 84.2 - - - +
278B GLN* 1.3 76.2 + - - +
279B LEU* 3.3 10.4 + - + +
326B PHE* 4.1 11.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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