Contacts of the helix formed by residues 483 - 503 (chain B) in PDB entry 2GRN
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 GLU 483 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B LYS* 2.7 19.6 + - + +
482B ASP* 1.3 75.2 - - - +
484B ALA* 1.3 75.6 + - - +
485B THR* 2.6 43.2 + - - +
486B VAL* 2.9 24.1 + - + +
487B ARG* 2.8 26.4 + - - +
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Residues in contact with ALA 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B GLU* 1.3 80.4 - - - +
485B THR* 1.3 68.8 + - + +
487B ARG* 3.7 21.7 + - - +
488B MET* 3.0 23.7 + - - +
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Residues in contact with THR 485 (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 26.7 - - - +
483B GLU* 2.6 34.6 + - - +
484B ALA* 1.3 80.6 - - + +
486B VAL* 1.3 55.3 + - - -
488B MET* 3.6 7.8 + - - +
489B ALA* 3.1 28.1 + - - +
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Residues in contact with VAL 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B PRO* 4.2 24.0 - - + +
446B LEU* 5.3 2.5 - - + -
447B LEU* 4.3 15.3 - - + -
479B VAL* 3.3 27.4 - - + +
481B LYS* 3.7 25.6 - - + +
483B GLU* 2.9 28.0 + - + +
485B THR* 1.3 74.5 - - - +
487B ARG* 1.3 67.8 + - - +
489B ALA* 3.2 5.6 + - - +
490B VAL* 2.9 30.2 + - + +
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Residues in contact with ARG 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B PHE* 3.7 20.6 - - + -
481B LYS 3.7 11.1 + - - +
482B ASP* 3.6 24.8 + - - -
483B GLU 2.8 42.1 + - - +
484B ALA* 3.7 22.4 + - - +
486B VAL* 1.3 72.7 - - - +
488B MET* 1.3 58.5 + - - +
490B VAL* 3.9 0.9 - - - +
491B GLN* 2.9 59.2 + - - +
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Residues in contact with MET 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B ALA 3.0 17.9 + - - +
485B THR* 3.9 6.5 - - - +
487B ARG* 1.3 77.6 - - - +
489B ALA* 1.3 59.6 + - + +
491B GLN* 3.9 8.4 - - - +
492B ASP* 2.9 56.8 + - - +
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Residues in contact with ALA 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LEU* 3.7 29.0 - - + +
447B LEU* 4.0 14.1 - - + -
453B SER* 4.8 11.7 + - - +
454B SER* 5.4 0.2 - - - -
485B THR 3.1 18.4 + - - +
486B VAL 3.2 4.0 + - - +
488B MET* 1.3 80.7 - - + +
490B VAL* 1.3 62.3 + - - +
492B ASP* 3.6 5.1 + - - +
493B ALA* 3.1 24.1 + - - +
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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 LEU* 3.7 19.7 - - + -
476B VAL* 3.8 19.5 - - + +
477B SER* 4.1 13.0 - - - -
479B VAL* 3.8 18.6 - - + -
480B PHE* 3.9 33.4 - - + -
486B VAL* 2.9 21.0 + - + +
487B ARG 4.0 2.9 - - - +
489B ALA* 1.3 72.8 - - - +
491B GLN* 1.3 68.2 + - + +
493B ALA* 3.2 2.6 + - - +
494B VAL* 2.9 29.4 + - + +
541B ALA* 4.8 5.6 - - + -
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Residues in contact with GLN 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B PHE* 4.6 13.0 - - + -
487B ARG* 2.9 52.7 + - + +
488B MET* 3.9 6.6 - - - +
490B VAL* 1.3 77.2 - - + +
492B ASP* 1.3 65.3 + - - +
494B VAL* 3.4 4.8 + - - +
495B ASP* 3.0 30.7 + - - +
540B MET 5.3 1.6 + - - +
541B ALA* 6.1 2.7 - - - +
544B HIS* 3.5 50.4 + - + +
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Residues in contact with ASP 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B SER* 6.1 0.2 - - - +
454B SER* 3.5 24.9 - - - +
488B MET* 2.9 50.7 + - - +
489B ALA* 4.1 4.6 - - - +
491B GLN* 1.3 77.4 - - - +
493B ALA* 1.3 56.9 + - - +
495B ASP* 3.4 10.9 + - - +
496B ALA* 3.0 23.9 + - - +
544B HIS* 5.8 0.3 + - - -
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Residues in contact with ALA 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B LEU* 5.0 4.5 - - + -
454B SER* 3.9 15.6 - - - +
457B ILE* 4.3 25.5 - - + +
476B VAL* 3.7 20.6 - - + -
489B ALA 3.1 19.3 + - - +
490B VAL 3.2 4.2 + - - +
492B ASP* 1.3 74.8 - - - +
494B VAL* 1.3 65.1 + - - +
496B ALA* 3.3 2.1 + - - +
497B LEU* 2.9 26.8 + - - +
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Residues in contact with VAL 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B PHE* 3.6 40.6 - - + +
476B VAL* 4.5 12.1 - - + -
477B SER* 5.1 0.2 - - - -
490B VAL* 2.9 27.6 + - + +
491B GLN* 3.7 6.7 - - - +
493B ALA* 1.3 74.9 - - - +
495B ASP* 1.3 61.0 + - - +
497B LEU* 3.8 5.5 - - - +
498B MET* 2.8 36.1 + - + +
541B ALA* 4.1 20.0 - - + +
544B HIS* 5.2 1.8 - - + -
545B MET* 4.3 11.0 - - + -
550B TYR* 4.1 11.4 - - - +
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Residues in contact with ASP 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B GLN 3.0 19.8 + - - +
492B ASP* 3.6 11.0 - - - +
493B ALA 3.2 0.2 - - - -
494B VAL* 1.3 76.7 - - - +
496B ALA* 1.3 56.1 + - - +
499B GLN* 2.9 34.4 + - - +
544B HIS* 2.7 35.9 + - - -
548B GLN* 3.5 9.6 - - - +
550B TYR* 2.7 39.4 + - + -
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Residues in contact with ALA 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B SER* 3.3 33.9 - - - +
455B VAL* 4.5 3.8 - - + +
458B ALA* 3.5 9.6 - - + +
492B ASP 3.0 16.9 + - - +
493B ALA 3.8 1.6 - - - +
495B ASP* 1.3 76.3 - - - +
497B LEU* 1.3 62.4 - - - +
499B GLN* 4.0 9.4 - - - +
500B LYS* 3.2 24.3 + - - +
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Residues in contact with LEU 497 (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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457B ILE* 4.7 9.6 - - + +
458B ALA* 3.8 13.8 - - + +
461B THR* 3.7 37.2 - - + +
463B THR* 4.1 11.2 - - + +
469B VAL* 4.0 11.0 - - + +
472B ALA* 3.8 10.1 - - + -
473B PHE* 3.7 35.2 - - + +
476B VAL* 5.6 2.2 - - + -
493B ALA 2.9 17.5 + - - +
494B VAL* 3.8 4.3 - - - +
496B ALA* 1.3 77.1 - - - +
498B MET* 1.3 71.0 + - + +
500B LYS* 3.3 4.3 + - - +
501B ALA* 3.1 26.2 + - - +
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Residues in contact with MET 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B VAL* 3.6 26.2 - - + -
473B PHE* 4.2 7.6 - - + -
494B VAL* 2.8 32.6 + - + +
497B LEU* 1.3 79.8 - - + +
499B GLN* 1.3 59.7 + - - +
501B ALA* 4.4 4.9 - - + -
502B PHE* 2.9 67.5 + - + +
507B PHE* 5.0 0.2 - - + -
512B PHE* 3.4 35.2 - - + -
545B MET* 3.9 15.7 - - - -
550B TYR* 3.5 20.4 - - + -
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Residues in contact with GLN 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ASP 2.9 22.0 + - - +
496B ALA* 4.0 8.0 - - - +
498B MET* 1.3 75.1 - - - +
500B LYS* 1.3 65.6 + - - +
503B ASN* 3.0 51.1 + - - +
550B TYR* 4.0 28.1 - - + +
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Residues in contact with LYS 500 (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 ALA* 2.9 37.0 + - + +
459B GLN* 3.8 15.8 + - - +
461B THR 3.8 6.3 + - - -
463B THR* 3.2 27.9 + - + +
496B ALA 3.2 16.1 + - - +
497B LEU 3.6 3.6 - - - +
499B GLN* 1.3 84.3 + - - +
501B ALA* 1.3 61.8 + - - +
503B ASN* 4.4 3.3 - - - +
504B SER* 3.8 14.4 + - - -
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Residues in contact with ALA 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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463B THR* 4.1 15.9 - - + +
469B VAL* 4.1 15.5 - - + -
497B LEU 3.1 16.3 + - - +
498B MET* 3.9 6.1 - - + +
500B LYS* 1.3 78.1 - - - +
502B PHE* 1.3 62.4 + - - +
504B SER* 3.2 8.6 + - - -
507B PHE* 3.0 55.9 - - + +
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Residues in contact with PHE 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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498B MET* 2.9 58.7 + - + +
499B GLN 4.3 0.7 - - - +
501B ALA* 1.3 72.8 - - - +
503B ASN* 1.3 63.6 + - - +
504B SER 3.2 8.5 + - - +
507B PHE* 4.1 14.4 - + - +
509B SER* 3.3 35.4 + - - -
512B PHE* 4.0 15.0 - + - -
545B MET* 4.2 12.6 - - - -
550B TYR* 3.7 30.5 - + + +
551B PHE* 4.3 4.3 - + - -
552B PRO* 3.7 29.8 - - + +
555B LEU* 4.0 9.9 - - + -
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Residues in contact with ASN 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B GLN* 3.0 44.3 + - - +
500B LYS* 4.4 4.0 - - - +
501B ALA 3.3 0.4 - - - -
502B PHE* 1.3 76.6 - - - +
504B SER* 1.3 61.1 + - - +
505B SER* 3.4 3.9 + - - -
550B TYR* 4.4 15.8 - - - +
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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
------------------------------------------------------------
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