Contacts of the helix formed by residues 487 - 506 (chain B) in PDB entry 6E7P
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 487 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B TYR* 3.8 17.1 + - - -
483B GLN* 4.0 3.2 - - - +
485B GLY 3.1 5.3 + - - -
486B ARG* 1.3 76.2 - - - +
488B SER* 1.3 57.2 + - - +
489B LEU* 3.0 13.1 + - - -
490B VAL* 3.1 19.2 + - - +
491B TRP 3.6 6.1 + - - -
384C ASP* 3.6 23.4 + - - -
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Residues in contact with SER 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B GLN 4.3 9.2 - - - -
484B GLN* 3.9 18.7 + - - +
485B GLY 4.1 4.2 + - - -
486B ARG 3.6 1.0 - - - -
487B SER* 1.3 72.2 - - - +
489B LEU* 1.3 59.0 + - - +
490B VAL 3.5 0.2 - - - -
491B TRP* 4.1 12.5 - - - +
492B LEU* 3.7 18.5 + - - +
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Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B SER* 3.0 2.7 + - - -
488B SER* 1.3 75.5 - - - +
490B VAL* 1.3 63.7 + - + +
491B TRP 3.2 0.2 - - - -
492B LEU* 3.1 15.6 + - + -
493B PHE* 2.9 26.9 + - + +
384C ASP* 5.3 6.3 - - + +
385C VAL* 4.8 19.3 - - + -
388C ILE* 3.8 26.2 - - + -
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Residues in contact with VAL 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B VAL* 4.1 18.6 - - + +
447B LEU* 4.2 13.4 - - + +
450B TYR* 3.9 29.4 - - + -
451B HIS* 5.7 1.6 - - - +
483B GLN* 5.9 4.9 - - + +
487B SER* 3.1 13.1 + - - +
489B LEU* 1.3 75.6 - - + +
491B TRP* 1.3 64.2 + - - +
493B PHE* 3.5 6.7 + - - +
494B SER* 3.0 23.0 + - - -
384C ASP* 3.6 40.4 - - + +
388C ILE* 5.0 7.4 - - + -
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Residues in contact with TRP 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B MET* 3.8 24.0 - - + -
481B GLN* 3.8 18.3 - - + +
483B GLN* 3.6 24.0 + - + +
484B GLN* 4.2 37.4 - - + +
487B SER 3.6 3.4 + - - -
488B SER* 4.2 16.4 - - - +
489B LEU 3.2 0.4 - - - -
490B VAL* 1.3 78.6 - - - +
492B LEU* 1.3 87.1 + - + +
494B SER* 2.4 32.2 + - - -
495B GLN* 3.0 42.1 + - + +
458C SER* 4.3 22.4 - - - -
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B SER* 3.7 12.2 + - - +
489B LEU* 3.1 18.2 + - + +
491B TRP* 1.3 98.9 - - + +
493B PHE* 1.3 62.1 + - - +
495B GLN* 3.8 5.0 + - + +
496B LEU* 3.5 26.7 + - + +
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Residues in contact with PHE 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B CYS* 4.0 19.7 - - - -
443B GLY* 6.0 0.2 - - - -
446B VAL* 3.5 37.5 - - + -
447B LEU* 5.3 2.9 - - + -
489B LEU* 2.9 17.0 + - + +
490B VAL* 3.8 8.5 - - - +
491B TRP 3.2 0.2 - - - -
492B LEU* 1.3 79.4 - - - +
494B SER* 1.3 53.3 + - - +
496B LEU* 3.1 14.8 + - + +
497B TYR* 2.6 63.0 + + + +
388C ILE* 4.0 25.1 - - + -
392C THR* 3.9 22.0 - - + -
395C LEU* 5.5 2.5 - - + -
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Residues in contact with SER 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LEU* 3.8 24.2 - - - -
480B MET* 4.0 23.7 - - - +
490B VAL 3.0 12.6 + - - -
491B TRP* 2.4 33.6 + - - -
493B PHE* 1.3 75.0 - - - +
495B GLN* 1.3 67.1 + - - +
497B TYR* 4.2 6.7 - - - -
498B LEU* 3.1 31.0 + - - +
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Residues in contact with GLN 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B PHE* 4.1 10.0 - - - -
480B MET* 4.7 6.4 - - - +
491B TRP* 3.0 54.0 + - + +
492B LEU* 4.1 6.1 - - + +
494B SER* 1.3 82.0 + - - +
496B LEU* 1.3 57.8 + - - +
498B LEU* 5.2 0.8 - - - +
499B TYR* 3.3 59.1 + - + +
458C SER* 4.8 3.8 + - - +
462C GLU* 3.2 31.4 + - - +
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 3.5 22.5 + - + +
493B PHE* 3.1 15.8 + - + +
495B GLN* 1.3 77.7 - - - +
497B TYR* 1.3 55.6 + - - +
499B TYR* 5.0 2.5 - - + -
500B SER* 2.7 42.4 + - - +
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Residues in contact with TYR 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B TYR* 2.3 63.0 + + + +
442B CYS* 4.2 9.6 - - + -
443B GLY* 3.4 26.7 + - - -
447B LEU* 4.0 15.9 - - + -
454B PHE* 5.2 3.6 - + - -
460B VAL* 5.4 0.5 - - - +
464B LEU* 3.9 19.4 - - + +
493B PHE* 2.6 48.5 + + + +
494B SER* 4.0 7.0 - - - +
496B LEU* 1.3 73.7 - - - +
498B LEU* 1.3 82.6 + - + +
500B SER* 3.2 13.7 + - - -
501B PHE* 3.5 15.2 + - + +
395C LEU* 5.1 2.0 - - + -
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Residues in contact with LEU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LEU* 5.3 1.1 - - + -
454B PHE* 4.7 15.5 - - + -
464B LEU* 5.1 4.3 - - + -
467B LEU* 4.7 23.5 - - + +
476B THR* 4.6 11.9 - - - +
477B PHE* 3.7 36.8 - - + -
480B MET* 4.3 24.7 - - + -
494B SER* 3.1 19.0 + - - +
497B TYR* 1.3 95.7 - - + +
499B TYR* 1.3 66.2 + - - +
501B PHE* 3.1 6.6 + - + +
502B ILE* 3.1 29.8 + - + +
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Residues in contact with TYR 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B PHE* 3.5 31.0 - + - -
495B GLN* 3.3 37.2 + - + +
496B LEU* 4.9 3.1 - - + +
498B LEU* 1.3 78.5 - - - +
500B SER* 1.3 60.0 + - - +
502B ILE* 4.1 2.6 - - - +
503B SER* 3.2 28.9 + - - -
436C TYR* 5.5 0.2 - - - -
461C SER* 2.7 43.3 + - - -
462C GLU* 3.7 9.7 - - + +
465C PHE* 3.7 30.1 - + + -
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Residues in contact with SER 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B TYR* 4.1 19.9 + - - -
496B LEU* 2.7 31.5 + - - -
497B TYR* 3.2 8.5 + - - -
499B TYR* 1.3 77.8 - - - +
501B PHE* 1.3 57.6 + - - +
503B SER* 4.6 1.5 - - - -
504B LEU* 3.3 22.1 + - - +
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Residues in contact with PHE 501 (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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436B TYR* 4.3 9.0 - + - -
439B TYR* 3.7 46.0 - + + -
464B LEU* 3.7 46.0 - - + -
467B LEU* 4.6 9.2 - - + -
468B ILE* 3.7 22.0 - - + -
497B TYR* 3.5 17.7 + + + +
498B LEU* 3.1 7.1 + - + +
500B SER* 1.3 78.8 + - - +
502B ILE* 1.3 68.8 + - - +
503B SER 3.2 1.1 - - - -
504B LEU* 3.1 12.5 + - + +
505B PHE* 3.3 49.1 + + - +
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Residues in contact with ILE 502 (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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467B LEU* 3.2 44.2 - - + +
468B ILE* 3.7 13.0 - - + -
473B MET* 3.7 19.5 - - + -
477B PHE* 5.1 5.2 - - + -
498B LEU 3.1 20.9 + - - +
499B TYR* 4.1 3.1 - - + +
501B PHE* 1.3 80.2 - - - +
503B SER* 1.3 60.3 + - - +
504B LEU 3.2 1.1 + - - -
506B ILE* 3.6 40.1 + - + +
507B TYR* 5.2 0.3 - - - -
465C PHE* 3.5 25.8 - - + -
469C ASN* 4.0 10.5 - - - +
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Residues in contact with SER 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B TYR 3.2 17.5 + - - -
500B SER* 4.6 2.2 - - - -
501B PHE 3.2 0.6 - - - -
502B ILE* 1.3 79.2 - - - +
504B LEU* 1.3 58.7 + - - +
507B TYR* 3.3 43.5 - - - +
508B MET* 5.0 5.5 - - - +
429C CYS* 5.8 3.6 - - - -
465C PHE* 4.2 13.0 - - - -
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Residues in contact with LEU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B ILE* 4.8 11.2 - - + -
439B TYR* 4.3 24.5 - - + +
500B SER 3.3 17.6 + - - +
501B PHE* 3.1 7.8 + - + +
503B SER* 1.3 81.3 - - - +
505B PHE* 1.3 84.8 + - + +
506B ILE 3.4 0.2 - - - -
507B TYR 4.1 0.2 - - - -
508B MET* 3.2 47.7 + - + -
509B VAL* 3.5 9.6 + - + +
418C LEU* 6.5 0.4 - - + -
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Residues in contact with PHE 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL* 3.7 29.8 - - + -
435B ILE* 4.9 13.0 - - + -
436B TYR* 3.9 28.9 - + + -
468B ILE* 3.6 49.4 - - + -
501B PHE* 3.3 33.2 + + - +
502B ILE 5.1 0.2 - - - +
504B LEU* 1.3 94.6 - - + +
506B ILE* 1.3 61.5 + - - +
509B VAL* 3.5 25.7 - - + +
510B LEU* 2.8 28.4 + - - +
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Residues in contact with ILE 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ILE* 3.6 22.4 - - - +
469B ASN 5.8 0.4 - - - -
470B GLY* 5.6 1.3 - - - +
473B MET* 5.3 0.2 - - + -
502B ILE* 3.6 37.8 + - + +
504B LEU 3.4 0.2 - - - -
505B PHE* 1.3 77.9 - - - +
507B TYR* 1.3 84.3 + - + +
508B MET 3.8 0.2 + - - -
510B LEU* 3.4 34.8 + - + +
511B SER* 4.0 6.1 + - - -
469C ASN* 3.5 29.8 - - + +
510C LEU* 4.4 13.7 - - + +
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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