Contacts of the helix formed by residues 448 - 465 (chain B) in PDB entry 6VW1
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 GLY 448 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B TYR* 4.4 14.4 + - - -
240B LEU* 4.6 3.1 - - - -
272B GLY 4.7 0.7 - - - +
273B ARG 4.3 5.2 - - - +
275B TRP* 4.6 22.6 + - - -
443B ALA 2.9 10.9 + - - -
444B LEU 3.7 15.4 + - - -
445B THR 4.4 0.2 - - - -
446B ILE 3.4 0.6 - - - -
447B VAL* 1.3 81.7 - - - +
449B THR* 1.3 58.3 + - - +
450B LEU 3.7 0.2 + - - -
451B PRO* 3.9 6.4 - - - +
452B PHE* 4.3 8.1 + - - +
485B VAL* 5.5 1.0 - - - +
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Residues in contact with THR 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ARG* 2.9 30.0 + - - +
274B PHE* 3.4 17.7 - - + -
445B THR 3.4 14.8 + - - +
446B ILE* 3.2 20.4 - - - +
447B VAL 3.1 1.0 - - - -
448B GLY* 1.3 80.2 - - - +
450B LEU* 1.3 64.8 + - + +
451B PRO 3.6 0.2 - - - -
452B PHE* 3.5 2.9 + - - +
453B THR* 2.7 47.0 + - - +
515B TYR* 5.8 4.0 - - + +
518B ARG* 4.9 6.7 - - - +
519B THR* 4.6 7.6 - - - +
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Residues in contact with LEU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 4.3 3.6 - - + -
233B ILE* 3.6 38.1 - - + -
446B ILE 3.4 16.4 - - - +
447B VAL* 3.4 10.7 + - + +
449B THR* 1.3 77.3 - - + +
451B PRO* 1.3 68.6 - - + +
453B THR* 3.4 3.5 + - - +
454B TYR* 2.9 31.2 + - - +
515B TYR 5.3 0.2 - - - -
516B TYR* 3.9 32.4 - - + +
519B THR* 3.6 31.4 - - + +
520B LEU* 5.1 0.9 - - + -
584B LEU* 4.1 21.1 - - + -
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Residues in contact with PRO 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 3.7 29.2 - - + -
233B ILE* 5.7 0.7 - - + -
237B TYR* 3.5 45.3 - - + -
447B VAL 3.3 15.0 - - - +
448B GLY 3.9 5.6 - - - +
449B THR 3.9 0.7 - - - -
450B LEU* 1.3 92.6 - - + +
452B PHE* 1.3 57.7 + - - +
454B TYR* 4.0 0.4 - - + +
455B MET* 2.9 34.5 + - - +
484B ILE* 4.3 2.6 - - + +
485B VAL* 3.6 18.3 - - + +
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Residues in contact with PHE 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B TRP* 3.5 33.4 - - + -
272B GLY* 3.9 17.3 - - - +
273B ARG* 3.5 36.8 - - + -
448B GLY 4.3 4.9 + - - +
449B THR* 3.5 10.5 + - - +
450B LEU 3.3 0.4 - - - -
451B PRO* 1.3 80.4 - - - +
453B THR* 1.3 65.1 + - - +
455B MET* 3.7 3.9 - - + +
456B LEU* 3.0 48.0 + - + +
477B TRP* 5.8 3.1 - + - -
481B LYS* 3.1 31.4 - - - -
485B VAL* 4.0 18.5 - - + +
503B LEU* 4.1 13.5 - - + -
512B PHE* 4.2 6.3 - + - -
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Residues in contact with THR 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ARG* 5.5 0.2 + - - -
449B THR* 2.7 33.8 + - - +
450B LEU* 3.8 4.9 - - - -
452B PHE* 1.3 76.4 - - - +
454B TYR* 1.3 65.6 + - - +
456B LEU* 3.8 1.0 - - - +
457B GLU* 2.9 24.3 + - - +
512B PHE* 3.4 52.5 - - + +
513B ILE* 4.5 2.0 - - - -
515B TYR* 4.2 8.2 - - + +
516B TYR* 3.9 26.5 - - + +
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Residues in contact with TYR 454 (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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226B VAL* 4.5 16.2 - - + -
227B GLU* 3.0 43.5 + - + +
230B PHE* 3.9 42.0 - + + -
450B LEU 2.9 17.6 + - - +
451B PRO 4.0 1.3 - - - +
453B THR* 1.3 77.1 - - - +
455B MET* 1.3 59.8 + - - +
457B GLU* 3.5 3.0 + - - -
458B LYS* 2.8 53.9 + - + +
461B TRP* 5.2 4.5 - + - -
484B ILE* 4.1 20.9 - - + -
513B ILE* 4.9 11.7 - - + -
516B TYR* 4.5 12.3 - + + -
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Residues in contact with MET 455 (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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451B PRO 2.9 16.3 + - - +
452B PHE* 3.7 9.4 - - + +
454B TYR* 1.3 74.5 - - - +
456B LEU* 1.3 78.0 + - + +
458B LYS* 3.3 1.9 + - - -
459B TRP* 2.9 23.7 + - - +
477B TRP* 4.2 18.8 - - + +
480B MET* 3.6 32.0 - - + +
481B LYS* 3.6 53.4 - - + +
484B ILE* 3.7 24.5 - - + -
485B VAL* 3.6 13.2 - - + -
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Residues in contact with LEU 456 (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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452B PHE* 3.0 26.5 + - + +
453B THR 3.8 2.9 - - - +
455B MET* 1.3 79.9 - - + +
457B GLU* 1.3 63.1 + - - +
459B TRP* 3.3 3.6 + - - +
460B ARG* 3.0 27.2 + - + +
477B TRP* 3.4 34.8 - - + -
500B PRO* 4.5 3.8 - - + -
503B LEU* 3.6 30.5 - - + -
506B VAL* 3.7 26.2 - - + -
512B PHE* 3.7 29.4 - - + -
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Residues in contact with GLU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TRP* 4.2 5.7 - - - -
453B THR 2.9 17.2 + - - +
454B TYR 4.1 2.2 - - - +
456B LEU* 1.3 78.6 - - - +
458B LYS* 1.3 58.1 + - - +
460B ARG* 2.7 32.7 + - - +
461B TRP* 2.9 69.4 + - + -
511B SER* 3.8 3.8 - - - -
512B PHE* 2.6 15.0 + - + -
513B ILE* 2.6 47.2 + - + +
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Residues in contact with LYS 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ILE* 5.4 3.6 - - + +
227B GLU* 3.2 23.8 - - - +
454B TYR* 2.8 48.1 + - + +
455B MET* 3.7 5.6 - - - +
457B GLU* 1.3 73.9 - - - +
459B TRP* 1.3 59.1 + - - +
461B TRP* 3.4 18.5 + - + +
462B MET* 2.9 69.8 + - - +
467B GLU* 4.9 1.0 + - - -
480B MET* 3.7 17.3 - - + -
484B ILE* 5.4 1.3 - - + -
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Residues in contact with TRP 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TYR* 4.4 18.4 - + - -
455B MET 2.9 17.0 + - - +
456B LEU 3.6 3.8 - - - +
458B LYS* 1.3 78.0 - - - +
460B ARG* 1.3 83.5 + - + +
462B MET* 3.4 3.9 + - - +
463B VAL* 2.9 50.4 + - + +
468B ILE* 4.0 16.4 - - + +
473B TRP* 3.1 54.3 + + + -
474B MET* 5.4 0.9 - - - -
477B TRP* 3.3 49.1 - + + +
480B MET* 3.6 16.7 - - + +
498B CYS* 5.4 1.1 - - - -
500B PRO* 3.5 30.1 - - + -
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Residues in contact with ARG 460 (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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180B TYR* 3.4 26.5 - - + +
183B TYR* 5.6 0.4 + - - -
203B TRP* 3.3 23.8 - - - -
456B LEU* 3.0 18.3 + - + +
457B GLU* 2.7 28.5 + - - +
459B TRP* 1.3 95.2 - - + +
461B TRP* 1.3 61.9 + - + +
463B VAL* 3.2 3.6 + - + +
464B PHE* 2.9 41.8 + - + -
505B HIS* 3.7 11.7 + - - +
506B VAL* 3.7 28.0 + - - +
509B ASP* 5.6 0.2 - - - +
510B TYR 2.9 20.8 + - - -
512B PHE* 3.0 35.6 - - - +
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Residues in contact with TRP 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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198B ASP* 4.7 2.3 - - - +
200B GLY* 3.9 14.3 + - - -
203B TRP* 5.1 7.8 - + - +
204B ARG* 3.2 53.6 + - + +
222B LEU* 4.2 9.6 - - + -
223B ILE* 4.1 23.3 - - + -
226B VAL* 4.4 16.6 - - + -
454B TYR* 5.2 3.6 - + - -
457B GLU* 2.9 47.1 + - + +
458B LYS* 3.7 24.9 - - + +
460B ARG* 1.3 77.6 - - + +
462B MET* 1.3 58.0 + - + +
464B PHE* 3.3 6.5 + + - +
465B LYS* 2.9 31.8 + - - +
513B ILE* 3.8 35.0 - - + -
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Residues in contact with MET 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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458B LYS* 2.9 56.2 + - - +
461B TRP* 1.3 77.8 - - + +
463B VAL* 1.3 63.0 + - - +
465B LYS* 3.3 7.6 + - + +
466B GLY 3.2 3.6 + - - -
467B GLU* 3.0 53.3 + - + +
468B ILE* 3.6 30.2 + - + -
476B LYS* 4.7 11.9 - - - +
480B MET* 4.6 10.8 - - - +
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Residues in contact with VAL 463 (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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180B TYR* 5.1 0.9 - - + -
184B VAL* 4.2 21.8 - - + +
188B ASN* 4.8 0.7 + - - -
459B TRP* 2.9 56.4 + - + +
460B ARG* 3.7 6.3 - - + +
462B MET* 1.3 76.2 - - - +
464B PHE* 1.3 65.3 + - + +
466B GLY* 3.1 13.5 + - - -
468B ILE* 4.1 18.8 - - + +
473B TRP* 3.6 41.3 - - + +
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Residues in contact with PHE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B TYR* 4.0 12.3 - + - -
183B TYR* 3.9 20.0 - + - -
184B VAL* 3.6 38.8 - - + -
188B ASN* 3.2 32.0 + - - +
192B ARG* 4.0 4.0 + - - -
198B ASP* 3.4 12.6 - - - +
199B TYR* 3.9 22.7 - + + -
200B GLY* 3.6 33.4 - - - +
203B TRP* 4.0 25.6 - + - -
460B ARG* 2.9 33.6 + - + +
461B TRP* 3.8 3.8 - + - +
463B VAL* 1.3 77.6 - - + +
465B LYS* 1.3 60.6 + - - +
466B GLY 3.1 1.6 + - - -
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Residues in contact with LYS 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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192B ARG* 5.3 5.0 + - - -
197B GLU* 3.6 22.4 + - - -
198B ASP* 3.6 20.5 + - - +
204B ARG* 5.5 8.5 - - - +
461B TRP 2.9 18.9 + - - +
462B MET* 3.7 7.9 - - - +
463B VAL 3.2 0.6 - - - -
464B PHE* 1.3 76.2 - - - +
466B GLY* 1.3 60.2 + - - +
467B GLU* 3.3 34.9 - - + +
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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