Contacts of the helix formed by residues 454 - 465 (chain B) in PDB entry 4X7C
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 454 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B MET* 3.7 41.1 - - + -
238B THR 3.6 7.9 - - - +
246B LEU* 3.8 14.1 - - + -
434B PHE* 3.8 31.4 - - + -
451B CYS* 4.4 3.3 - - - -
453B LEU* 1.3 86.4 - - - +
455B GLN* 1.3 65.8 + - - +
456B GLU* 4.1 1.1 - - - +
457B TRP* 3.0 38.6 + - + +
458B VAL* 3.2 10.9 + - - +
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Residues in contact with GLN 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B THR* 2.9 23.6 + - - +
239B ASN 4.1 9.4 - - - +
240B SER* 3.3 29.1 - - - +
264B GLY* 4.8 2.1 + - - -
276B THR* 5.0 0.9 - - - +
277B GLN 2.8 28.9 + - - +
278B LEU* 2.9 23.8 + - - +
279B SER 3.9 1.8 - - - +
280B PRO* 3.9 26.7 - - + -
283B ILE* 4.1 8.6 - - + +
453B LEU 3.6 1.6 + - - -
454B PRO* 1.3 73.6 - - - +
456B GLU* 1.3 61.2 + - - +
458B VAL* 3.2 15.8 + - - +
459B GLN* 2.9 28.8 + - - +
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Residues in contact with GLU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A SER* 5.2 0.2 - - - -
280A PRO* 4.7 1.0 - - - +
459A GLN* 3.6 26.7 + - - +
463A GLN* 5.7 2.2 - - - +
230B PRO* 4.0 3.8 - - + +
232B LEU* 3.8 27.4 - - + -
236B GLU 4.0 3.9 - - - +
237B MET* 3.3 23.0 - - + +
238B THR* 2.7 52.6 + - - +
280B PRO* 5.7 1.6 - - - +
454B PRO* 3.1 0.4 - - - +
455B GLN* 1.3 71.4 + - - +
457B TRP* 1.3 63.9 + - + +
459B GLN* 3.4 14.8 + - - +
460B HIS* 2.8 29.6 + - - +
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Residues in contact with TRP 457 (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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229B VAL* 4.4 7.0 - - + -
230B PRO* 3.4 33.2 + - + +
232B LEU 5.6 0.4 + - - -
237B MET* 3.4 28.0 - - + +
434B PHE* 4.1 18.2 - + - -
453B LEU* 4.1 13.2 - - + -
454B PRO* 3.0 29.4 + - + +
456B GLU* 1.3 75.6 - - - +
458B VAL* 1.3 66.0 + - - +
460B HIS* 3.2 5.4 + - - +
461B PHE* 2.9 53.9 + + + -
475B LEU* 3.7 31.6 - - + -
491B LEU* 4.3 14.4 - - + -
497B VAL* 4.3 3.6 - - + -
515B PHE* 3.6 38.6 - + + -
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Residues in contact with VAL 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B GLY* 4.2 24.7 - - - -
266B CYS* 4.0 23.5 - - + -
272B LEU* 3.5 29.2 - - + -
276B THR* 3.9 10.5 - - + -
278B LEU* 4.4 4.9 - - + -
453B LEU* 4.2 11.0 - - + -
454B PRO 3.2 12.9 + - - +
455B GLN* 3.2 24.9 + - - +
457B TRP* 1.3 76.2 - - - +
459B GLN* 1.3 64.4 + - - +
461B PHE* 4.0 1.5 - - - -
462B TYR* 3.1 23.0 + - - +
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Residues in contact with GLN 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 5.4 4.3 - - + +
236A GLU 5.6 0.4 + - - -
456A GLU* 3.6 33.4 + - - +
459A GLN* 4.0 10.3 + - - +
278B LEU* 2.9 45.0 + - + +
280B PRO* 4.0 12.2 - - - +
455B GLN* 2.9 21.9 + - - +
456B GLU* 3.6 28.1 + - - +
458B VAL* 1.3 76.2 - - - +
460B HIS* 1.3 62.6 - - - +
462B TYR* 3.7 1.7 - - - +
463B GLN* 3.2 40.1 + - - +
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Residues in contact with HIS 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A GLN* 4.9 8.0 + - - -
464A GLU* 5.5 7.0 - - - -
228B THR* 2.8 49.2 + - - -
229B VAL* 4.0 2.1 - - - -
230B PRO* 3.7 31.8 - - + +
456B GLU 2.8 18.2 + - - +
457B TRP 3.2 4.0 + - - +
459B GLN* 1.3 77.1 - - - +
461B PHE* 1.3 63.7 + + + +
463B GLN* 3.2 7.1 + - - +
464B GLU* 2.9 55.9 + - + +
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Residues in contact with PHE 461 (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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227B PHE* 3.6 27.1 - + - -
228B THR 3.8 9.0 - - - -
229B VAL* 4.2 6.5 - - + -
266B CYS* 4.2 8.1 - - - -
267B THR 3.5 24.0 - - - +
268B THR* 3.5 23.6 - - + +
269B ASP 4.0 0.2 - - - -
270B GLY* 3.2 11.8 + - - +
453B LEU* 4.4 13.9 - - + -
457B TRP* 2.9 52.5 + + + +
458B VAL* 4.1 2.9 - - - +
460B HIS* 1.3 82.7 - + + +
462B TYR* 1.3 58.1 + - - +
464B GLU* 4.7 3.1 - - - +
465B ALA* 2.8 27.7 + - - +
491B LEU* 3.8 26.2 - - + -
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Residues in contact with TYR 462 (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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231A ILE* 5.0 6.8 - - + +
232A LEU* 4.2 15.3 - - + -
236A GLU* 3.6 16.8 + - - -
266B CYS* 5.1 0.2 - - - -
270B GLY* 3.6 25.6 - - - +
272B LEU* 3.9 29.8 - - + -
278B LEU* 3.6 33.9 - - + -
458B VAL 3.1 17.3 + - - +
459B GLN 3.7 3.4 - - - +
460B HIS 3.3 0.2 - - - -
461B PHE* 1.3 80.0 - - - +
463B GLN* 1.3 66.0 + - + +
465B ALA* 4.0 9.9 + - - +
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Residues in contact with GLN 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PRO* 3.0 35.7 - - - +
231A ILE* 3.3 35.8 + - + +
232A LEU* 3.8 39.0 - - + +
456A GLU* 5.7 1.8 - - - +
460A HIS* 4.8 9.3 + - - +
225B LYS* 4.3 3.5 + - - -
459B GLN* 3.2 27.3 + - - +
460B HIS* 3.7 5.8 - - - +
462B TYR* 1.3 77.7 - - + +
464B GLU* 1.3 73.0 + - + +
465B ALA* 4.4 2.4 - - - +
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Residues in contact with GLU 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A HIS* 5.3 8.7 - - - -
225B LYS* 2.8 46.2 + - - +
226B PRO 4.7 6.9 - - - +
227B PHE* 6.3 1.3 - - + -
228B THR* 4.3 9.9 + - - +
460B HIS* 2.9 49.7 + - + +
461B PHE* 4.3 3.1 - - + +
463B GLN* 1.3 82.9 - - + +
465B ALA* 1.3 70.4 + - - +
466B ALA* 3.1 11.6 + - + +
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Residues in contact with ALA 465 (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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225B LYS* 4.8 1.9 - - - +
269B ASP* 3.3 23.4 - - - +
270B GLY* 5.2 0.7 - - - -
461B PHE 2.8 17.9 + - - -
462B TYR 4.1 11.2 - - - +
463B GLN 4.4 2.5 - - - +
464B GLU* 1.3 74.2 - - - +
466B ALA* 1.3 62.7 + - - +
467B PRO* 3.6 7.4 - - - +
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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