Contacts of the helix formed by residues 481 - 500 (chain B) in PDB entry 4QGC
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 ALA 481 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516A ARG* 6.0 1.1 - - - +
479B GLN* 3.9 3.3 - - - +
480B GLU* 1.3 78.6 - - - +
482B TRP* 1.3 65.1 + - - +
483B ALA* 4.6 3.4 - - + +
484B GLU* 3.0 33.4 + - + +
485B ASP* 3.0 21.3 + - - +
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Residues in contact with TRP 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A TRP* 6.1 1.6 - + - -
483A ALA* 6.1 2.5 - - + -
515A TRP* 3.6 30.7 - + - -
479B GLN 5.1 1.1 - - - -
480B GLU 3.6 4.6 + - - -
481B ALA* 1.3 71.8 - - - +
483B ALA* 1.3 74.9 + - + +
485B ASP* 3.1 9.3 + - + +
486B VAL* 3.0 43.2 + - + +
489B ARG* 4.7 2.7 - - - -
513B THR* 4.9 0.7 - - - -
514B GLY* 3.4 24.9 - - - -
515B TRP* 3.0 35.9 - + - -
516B ARG* 3.9 6.5 - - + -
517B PRO* 3.5 46.7 - - + +
1003B SO4 3.0 35.2 + - - -
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Residues in contact with ALA 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A TRP* 6.1 3.4 - - + -
515A TRP* 4.2 8.8 - - + -
516A ARG* 3.5 37.0 + - - +
481B ALA* 3.3 3.1 - - + -
482B TRP* 1.3 95.9 - - + +
484B GLU* 1.3 57.6 + - - +
486B VAL* 3.4 3.2 + - - +
487B ASP* 3.1 32.7 + - - +
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Residues in contact with GLU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A ARG* 3.2 26.4 + - - +
479B GLN* 4.1 15.9 + - + +
481B ALA* 3.0 31.5 + - + +
483B ALA* 1.3 76.4 - - - +
485B ASP* 1.3 60.7 + - - +
487B ASP* 3.5 6.0 + - + +
488B LEU* 3.1 26.0 + - - +
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Residues in contact with ASP 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ARG* 2.9 42.5 + - - -
478B VAL* 3.3 10.1 - - + +
479B GLN* 2.9 42.7 + - + +
481B ALA 3.0 9.2 + - - +
482B TRP* 3.1 12.2 + - + +
484B GLU* 1.3 74.4 - - - +
486B VAL* 1.3 65.2 + - - +
488B LEU* 3.5 3.7 + - - +
489B ARG* 3.1 47.8 + - - +
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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
----------------------------------------------------------
515A TRP* 4.0 20.2 - - + -
431B LEU* 3.8 17.9 - - + -
482B TRP* 3.0 48.2 + - + +
483B ALA 3.6 7.9 - - - +
485B ASP* 1.3 75.4 - - - +
487B ASP* 1.3 60.0 + - - +
489B ARG* 3.2 22.9 + - - +
490B VAL* 2.9 28.7 + - + +
513B THR* 3.9 17.5 - - + -
526B ARG* 4.1 9.9 - - - +
1003B SO4 4.3 0.9 - - - +
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Residues in contact with ASP 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A TRP* 2.9 28.2 + - - -
516A ARG* 3.2 30.3 + - - +
483B ALA 3.1 12.6 + - - +
484B GLU* 3.8 7.0 - - + +
485B ASP 3.4 0.2 - - - -
486B VAL* 1.3 76.6 - - - +
488B LEU* 1.3 58.6 + - - +
490B VAL* 3.5 5.6 + - - +
491B ASN* 2.8 35.9 + - - +
526B ARG* 4.4 6.6 + - - -
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Residues in contact with LEU 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B ARG* 4.5 6.5 - - - +
474B CYS* 5.5 2.2 - - - -
476B ASP* 3.7 41.3 - - + +
477B PRO 4.3 3.1 - - - +
479B GLN* 3.9 31.0 - - + +
484B GLU 3.1 17.9 + - - +
485B ASP* 3.6 6.5 - - - +
486B VAL 3.2 0.4 - - - -
487B ASP* 1.3 78.3 - - - +
489B ARG* 1.3 56.4 + - + +
491B ASN* 3.4 8.4 + - + +
492B PHE* 2.9 27.8 + - + +
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Residues in contact with ARG 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B LEU* 3.7 31.9 - - + +
432B THR 5.6 1.8 + - - +
433B LYS* 5.6 2.4 - - - +
453B VAL* 3.8 26.3 + - + +
454B THR* 5.9 1.6 - - - +
455B ARG* 3.6 25.0 - - - +
474B CYS* 4.0 21.3 - - - -
482B TRP* 4.4 2.0 - - - +
485B ASP* 3.1 34.4 + - - +
486B VAL* 3.2 24.9 + - - +
488B LEU* 1.3 76.8 - - - +
490B VAL* 1.3 64.7 + - - +
492B PHE* 3.3 8.2 + - - +
493B ALA* 3.1 21.3 + - - +
1003B SO4 2.7 42.0 + - - -
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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
----------------------------------------------------------
429B ILE* 4.3 3.8 - - + +
431B LEU* 3.9 14.8 - - + -
486B VAL* 2.9 24.2 + - + +
487B ASP* 3.8 5.8 - - - +
489B ARG* 1.3 75.2 - - - +
491B ASN* 1.3 60.8 + - - +
493B ALA* 3.0 9.1 + - - +
494B MET* 2.9 49.6 + - + +
511B VAL* 3.8 27.4 - - + -
526B ARG* 3.8 26.5 - - - +
528B VAL* 5.5 2.0 - - + -
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Residues in contact with ASN 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B ASP* 2.8 22.1 + - - +
488B LEU* 3.6 10.5 - - + +
490B VAL* 1.3 76.8 - - - +
492B PHE* 1.3 62.7 + - - +
494B MET* 3.2 12.1 + - - +
495B ASN* 3.1 40.1 + - - +
531B PRO* 4.8 15.1 - - - +
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Residues in contact with PHE 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PRO* 3.6 31.2 - - + -
103B ILE* 4.1 27.6 - - + -
453B VAL* 4.4 3.6 - - + -
472B VAL* 3.4 32.8 - - + -
473B LEU 3.5 22.4 - - - -
474B CYS* 3.6 26.5 - - + -
475B LYS 5.3 0.7 - - - -
476B ASP* 6.1 1.1 - - - +
488B LEU* 2.9 15.4 + - + +
489B ARG* 3.4 10.3 - - - +
491B ASN* 1.3 74.5 - - - +
493B ALA* 1.3 61.4 + - - +
495B ASN* 3.4 9.6 + - + +
496B VAL* 3.1 33.3 + - + +
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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
----------------------------------------------------------
429B ILE* 3.7 25.8 - - + -
451B ILE* 3.9 20.2 - - + +
453B VAL* 3.6 28.5 - - + -
472B VAL* 5.2 0.4 - - - -
489B ARG 3.1 5.6 + - - +
490B VAL 3.0 9.8 + - - +
492B PHE* 1.3 74.0 - - - +
494B MET* 1.3 61.4 + - - +
496B VAL* 3.4 5.0 + - - +
497B GLY* 2.9 26.7 + - - -
503B PHE* 3.9 0.5 - - - -
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Residues in contact with MET 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ILE* 4.2 6.7 - - + -
490B VAL* 2.9 35.4 + - + +
491B ASN* 3.2 17.0 + - - +
493B ALA* 1.3 78.1 - - - +
495B ASN* 1.3 58.6 + - - +
497B GLY 3.3 0.7 + - - -
498B LYS* 3.0 45.4 + - - +
503B PHE* 3.5 17.6 - - + -
509B VAL* 3.6 32.1 - - + -
511B VAL* 4.8 0.7 - - + -
528B VAL* 3.6 23.3 - - + -
529B PRO 4.4 0.7 - - - +
530B VAL* 4.3 2.2 - - - -
531B PRO* 3.8 32.8 - - + -
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Residues in contact with ASN 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ILE* 3.7 25.8 - - + +
491B ASN* 3.1 27.6 + - - +
492B PHE* 3.8 11.3 - - + +
493B ALA 3.3 0.2 - - - -
494B MET* 1.3 73.7 - - - +
496B VAL* 1.3 66.2 + - - +
498B LYS* 3.4 21.5 + - - +
499B ALA* 3.1 24.6 + - - +
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Residues in contact with VAL 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ILE* 3.7 37.9 - - + +
451B ILE* 5.1 4.3 - - + -
470B PHE* 3.6 32.8 - - + -
472B VAL* 3.6 25.6 - - + -
492B PHE* 3.1 27.8 + - + +
493B ALA* 3.7 6.3 - - - +
495B ASN* 1.3 74.2 - - - +
497B GLY* 1.3 60.2 + - - +
499B ALA* 3.2 2.1 + - - +
500B ARG* 2.9 32.6 + - + +
502B PHE* 5.4 0.2 - - + -
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Residues in contact with GLY 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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451B ILE* 4.2 2.2 - - - +
493B ALA 2.9 11.4 + - - -
494B MET 3.8 0.2 - - - -
496B VAL* 1.3 78.0 - - - +
498B LYS* 1.3 55.6 + - - +
500B ARG 3.5 0.2 + - - -
501B GLY 3.0 6.2 + - - -
502B PHE* 2.8 44.2 + - - +
503B PHE* 3.5 31.1 + - - -
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Residues in contact with LYS 498 (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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494B MET* 3.0 26.3 + - - +
495B ASN* 3.4 28.6 + - - +
496B VAL 3.3 0.2 - - - -
497B GLY* 1.3 75.6 - - - +
499B ALA* 1.3 63.6 + - - +
501B GLY* 3.2 12.3 + - - -
503B PHE* 3.5 24.8 - - + +
504B LYS* 4.5 2.7 - - + -
505B LYS* 4.5 13.9 - - + +
530B VAL* 4.0 7.6 - - - -
531B PRO* 3.2 33.6 + - - +
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Residues in contact with ALA 499 (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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103B ILE* 4.1 16.2 - - + +
104B LEU* 4.2 17.5 - - + +
495B ASN 3.1 16.2 + - - +
496B VAL 3.2 3.8 + - - +
498B LYS* 1.3 79.0 - - - +
500B ARG* 1.3 64.5 + - + +
501B GLY 3.7 0.2 + - - -
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Residues in contact with ARG 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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103B ILE 4.6 4.2 + - - -
104B LEU* 2.9 55.0 + - - +
106B ARG* 3.5 18.6 - - - +
470B PHE* 3.8 33.8 - - + -
496B VAL* 2.9 21.6 + - + +
497B GLY 4.1 1.6 - - - +
498B LYS 3.2 0.2 - - - -
499B ALA* 1.3 80.6 + - + +
501B GLY* 1.3 60.3 + - - +
502B PHE* 3.9 27.8 - - + -
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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