Contacts of the helix formed by residues 494 - 509 (chain K) in PDB entry 5G04
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 ASN 494 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489K HIS* 3.0 16.3 + - - +
490K SER 4.4 0.2 + - - -
492K MET* 3.6 36.6 + - - +
493K GLY* 1.3 78.9 - - - +
495K PHE* 1.3 58.8 + - - +
496K GLU* 3.4 2.7 - - - -
497K ASN* 3.3 29.8 + - + +
498K ALA* 3.1 28.2 + - - +
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Residues in contact with PHE 495 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490K SER* 3.7 21.1 - - - -
493K GLY* 3.3 31.1 + - - -
494K ASN* 1.3 68.9 - - - +
496K GLU* 1.3 59.6 + - - +
498K ALA* 3.4 3.9 + - - +
499K VAL* 2.9 36.2 + - - +
522K CYS* 4.0 26.7 - - - +
525K MET* 3.4 50.9 - - + -
526K TYR* 3.9 19.1 - - + -
19W PHE* 3.6 34.1 - + - -
22W ILE* 5.9 2.0 - - + -
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Residues in contact with GLU 496 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638H TRP* 5.9 3.3 - - - -
660H LYS* 5.3 14.8 - - + +
663H ASP* 5.5 7.7 - - - +
494K ASN 3.4 0.2 - - - -
495K PHE* 1.3 78.4 - - - +
497K ASN* 1.3 84.5 + - - +
499K VAL* 3.5 4.8 + - - +
500K ASP* 3.4 20.6 + - - +
526K TYR* 3.3 40.6 - - + +
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Residues in contact with ASN 497 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489K HIS* 4.3 22.7 + - + +
494K ASN* 3.3 36.1 + - - +
496K GLU* 1.3 91.0 - - - +
498K ALA* 1.3 65.5 + - - +
500K ASP* 3.3 14.5 + - - +
501K TYR* 3.2 26.0 - - + -
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Residues in contact with ALA 498 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486K GLY* 3.4 24.7 - - - +
489K HIS* 3.7 7.8 - - + +
490K SER* 3.7 21.8 - - - +
494K ASN 3.1 16.9 + - - +
495K PHE* 3.7 6.7 - - - +
497K ASN* 1.3 74.8 - - - +
499K VAL* 1.3 65.3 + - - +
501K TYR* 3.1 4.4 + - - +
502K PHE* 3.0 30.7 + - + -
522K CYS* 4.7 3.8 - - - -
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Residues in contact with VAL 499 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638H TRP* 4.8 1.8 - - + -
656H MET* 4.9 4.5 - - + -
660H LYS* 3.4 31.6 - - + +
495K PHE 2.9 22.7 + - - +
496K GLU* 3.5 5.6 + - - +
497K ASN 3.3 0.2 - - - -
498K ALA* 1.3 72.8 - - - +
500K ASP* 1.3 67.6 + - - +
502K PHE* 3.4 1.9 + - - +
503K HIS* 3.1 33.3 + - + -
519K LEU* 4.0 9.6 - - + -
522K CYS* 4.0 22.9 - - + +
523K ILE* 3.5 32.5 - - + -
526K TYR* 5.0 2.0 - - + -
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Residues in contact with ASP 500 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628H ILE* 3.4 25.3 - - - +
632H PRO* 4.1 20.3 - - - +
638H TRP* 4.1 18.5 - - + -
496K GLU* 3.4 13.0 + - - +
497K ASN* 3.3 13.6 + - - +
498K ALA 3.2 0.2 - - - -
499K VAL* 1.3 81.5 - - - +
501K TYR* 1.3 74.8 + - - +
503K HIS* 3.2 4.6 + - - +
504K THR* 3.1 25.2 + - - +
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Residues in contact with TYR 501 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H ASP* 2.7 44.7 + - - -
131H LEU* 4.4 11.2 - - + +
482K TYR* 3.9 25.5 - + - +
485K ILE* 3.8 17.2 - - + +
486K GLY* 3.6 21.3 - - - +
489K HIS* 3.6 32.3 + + - -
497K ASN* 3.2 25.3 + - + -
498K ALA 3.1 3.2 + - - +
500K ASP* 1.3 89.2 - - - +
502K PHE* 1.3 64.5 + - - +
504K THR* 3.1 12.2 + - + -
505K ALA* 3.1 23.0 + - - +
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Residues in contact with PHE 502 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483K SER* 3.6 24.7 - - - -
486K GLY* 3.4 21.8 - - - -
487K TYR* 3.3 22.4 - - + -
490K SER* 4.7 0.4 - - - -
498K ALA* 3.0 29.4 + - + +
499K VAL* 3.4 1.1 + - - -
501K TYR* 1.3 75.2 - - - +
503K HIS* 1.3 62.4 + - - +
505K ALA* 3.5 4.5 + - - +
506K LEU* 3.1 30.9 + - - +
514K PHE* 4.2 3.6 - + - -
515K SER* 3.7 27.4 - - - +
518K MET* 3.3 37.5 - - + -
519K LEU* 3.9 29.4 - - + -
522K CYS* 4.5 15.7 - - - -
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Residues in contact with HIS 503 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625H ARG* 3.3 55.0 + - + +
628H ILE* 5.2 8.5 - - + -
638H TRP* 4.1 18.4 - + - -
641H LEU* 4.4 12.8 - - + +
645H TYR* 4.3 5.4 - - - -
657H HIS* 3.3 29.2 - + - -
499K VAL* 3.1 34.1 + - + +
500K ASP* 3.3 9.4 - - - +
501K TYR 3.2 0.2 - - - -
502K PHE* 1.3 74.8 - - - +
504K THR* 1.3 65.7 + - + +
506K LEU* 3.2 4.1 + - - +
507K GLY 3.0 17.5 + - - -
519K LEU* 3.8 16.7 - - + +
523K ILE* 4.6 0.8 - - + +
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Residues in contact with THR 504 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625H ARG 4.8 2.9 - - - -
628H ILE* 4.9 3.4 - - + +
629H ARG* 4.1 42.2 - - + +
632H PRO* 6.4 0.2 - - + -
482K TYR* 3.3 27.6 - - + -
500K ASP* 3.1 30.7 + - - +
501K TYR* 3.1 14.9 + - + +
503K HIS* 1.3 75.4 - - - +
505K ALA* 1.3 65.5 + - - +
507K GLY* 3.2 3.5 + - - +
508K LEU* 3.1 24.6 + - - +
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Residues in contact with ALA 505 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479K ALA* 3.5 30.7 - - + +
482K TYR* 3.7 10.1 - - + -
483K SER* 3.6 25.8 - - - +
501K TYR 3.1 8.1 + - - +
502K PHE* 3.8 6.1 - - - +
503K HIS 3.3 0.2 - - - -
504K THR* 1.3 81.0 + - - +
506K LEU* 1.3 59.2 + - - +
508K LEU* 3.3 5.7 + - - +
509K ARG* 3.1 26.0 + - - +
515K SER* 4.6 6.2 + - - +
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Residues in contact with LEU 506 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622H ALA* 5.5 1.7 - - - +
625H ARG* 3.6 36.4 + - - +
502K PHE 3.1 14.2 + - - +
503K HIS 3.2 5.1 + - - +
505K ALA* 1.3 75.4 - - - +
507K GLY* 1.3 62.7 + - - +
509K ARG 3.2 25.8 - - - +
510K ARG* 3.3 15.0 + - - +
512K ASP 3.8 2.5 - - - +
515K SER* 3.3 33.4 - - - +
516K VAL* 3.6 35.9 - - + +
519K LEU* 3.7 22.9 - - + -
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Residues in contact with GLY 507 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LEU 4.9 0.3 - - - +
103E LEU 3.0 26.4 - - - +
104E GLY* 3.8 0.9 - - - -
622H ALA* 4.4 3.5 - - - +
625H ARG* 3.9 14.1 - - - +
626H ASN* 3.3 28.6 + - - +
629H ARG* 6.2 0.2 - - - -
503K HIS 3.0 12.2 + - - -
504K THR 3.2 4.6 + - - -
506K LEU* 1.3 77.9 - - - +
508K LEU* 1.3 59.0 + - - +
509K ARG 3.6 0.2 + - - -
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Residues in contact with LEU 508 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LEU 5.4 4.7 - - - +
104E GLY* 3.4 18.6 - - - +
107E PRO* 4.3 8.5 - - - +
626H ASN* 4.9 0.7 - - - +
629H ARG* 3.7 33.0 - - - +
477K GLN* 3.6 30.3 - - + +
478K ASN 3.5 33.2 - - - +
479K ALA* 3.9 8.5 - - + +
482K TYR* 3.7 22.0 - - + -
504K THR 3.1 8.5 + - - +
505K ALA 3.3 7.6 + - - +
507K GLY* 1.3 76.2 - - - +
509K ARG* 1.3 59.5 + - - +
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Residues in contact with ARG 509 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E GLY 3.6 4.7 - - - -
107E PRO* 4.4 22.6 - - + +
479K ALA* 3.6 23.8 - - + -
505K ALA 3.1 11.4 + - - +
506K LEU* 3.2 12.1 - - - +
508K LEU* 1.3 79.0 - - - +
510K ARG* 1.3 62.3 + - - +
511K ASP* 2.9 44.0 + - - +
512K ASP* 3.5 35.3 + - + +
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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