Contacts of the helix formed by residues 503 - 513 (chain A) in PDB entry 3HB0
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 503 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502A ASP* 1.3 87.6 - - - +
504A VAL* 1.3 61.8 + - - -
505A GLU 3.5 1.8 - - - -
506A GLU* 3.0 35.7 + - - +
507A GLU* 3.5 12.6 + - - +
517A PHE* 4.3 3.3 - - - -
430B LYS* 4.0 5.2 - - - -
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Residues in contact with VAL 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A GLY* 1.3 69.6 - - - -
505A GLU* 1.3 79.0 + - + +
507A GLU* 2.9 13.8 + - - +
508A GLN* 2.8 25.0 + - - +
430B LYS* 4.5 18.6 - - + +
433B ASN* 3.5 35.7 - - + +
434B LEU* 4.1 31.0 - - + +
437B SER* 4.1 13.9 - - - +
534B GLU* 5.9 2.0 - - - +
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Residues in contact with GLU 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A THR* 3.5 22.7 - - - +
475A ALA* 4.6 1.7 - - - +
479A GLY* 3.9 6.6 - - - -
480A LYS* 3.1 49.1 + - + +
481A GLU 5.9 0.2 - - - +
503A GLY 3.5 0.2 - - - -
504A VAL* 1.3 83.7 - - + +
506A GLU* 1.3 60.9 + - + +
508A GLN* 3.2 6.0 + - - +
509A GLY* 2.9 27.7 + - - -
437B SER* 5.1 4.3 - - - -
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Residues in contact with GLU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ASP* 3.3 8.0 - - + +
480A LYS* 3.0 40.3 + - + +
484A PHE* 3.4 16.5 - - + -
499A VAL* 3.7 9.3 - - + +
500A ILE 5.5 0.2 - - - +
501A GLY* 2.8 32.6 - - - -
503A GLY* 3.0 37.3 + - - +
505A GLU* 1.3 75.2 - - + +
507A GLU* 1.3 55.3 + - - +
510A ALA* 3.1 25.5 + - - +
517A PHE* 4.0 7.6 - - + -
701A MG 3.2 16.1 - - - -
801A BEF 4.0 0.7 - - - -
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Residues in contact with GLU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A GLY 3.5 5.9 + - - +
504A VAL* 2.9 16.6 + - - +
506A GLU* 1.3 76.8 - - - +
508A GLN* 1.3 65.7 + - - +
510A ALA* 3.2 4.7 + - - +
511A LYS* 3.1 45.2 + - + +
517A PHE* 3.5 47.5 - - + -
519A ARG* 3.1 32.0 + - - +
434B LEU* 5.9 2.4 - - - +
534B GLU* 4.9 0.5 - - - +
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Residues in contact with GLN 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504A VAL 2.8 18.7 + - - +
505A GLU* 3.6 4.3 - - - +
507A GLU* 1.3 70.2 - - - +
509A GLY* 1.3 66.5 + - - +
511A LYS* 3.1 26.3 + - - +
512A LYS* 3.1 54.2 + - - +
434B LEU* 6.1 0.3 - - - +
437B SER* 3.7 41.1 + - - +
438B ARG* 4.7 4.0 - - - +
439B PRO* 4.5 11.3 - - - +
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Residues in contact with GLY 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A GLU* 4.6 19.5 - - - -
484A PHE* 3.9 15.4 - - - -
505A GLU 2.9 16.0 + - - -
506A GLU 3.9 1.6 - - - -
507A GLU 3.3 0.2 - - - -
508A GLN* 1.3 78.2 - - - +
510A ALA* 1.3 61.4 + - - +
512A LYS* 3.4 4.7 + - - -
513A HIS* 3.3 27.2 + - - -
515A MET* 3.7 3.1 - - - +
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Residues in contact with ALA 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A PHE* 4.0 0.2 - - - -
499A VAL* 3.9 21.1 - - + -
506A GLU 3.1 14.3 + - - +
507A GLU 3.2 10.5 + - - +
509A GLY* 1.3 78.1 - - - +
511A LYS* 1.3 56.0 + - + +
513A HIS 3.4 1.2 + - - -
514A ASN* 3.1 6.4 + - - -
515A MET* 2.8 58.1 + - - +
517A PHE* 4.1 11.4 - - + -
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Residues in contact with LYS 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507A GLU* 3.1 38.0 + - + +
508A GLN* 3.1 28.4 + - - +
510A ALA* 1.3 74.9 - - + +
512A LYS* 1.3 63.3 + - - +
513A HIS 2.9 6.3 + - - -
514A ASN* 3.0 20.5 + - - +
517A PHE* 6.4 0.9 - - + -
434B LEU* 6.1 3.0 - - - +
534B GLU 5.6 3.8 + - - -
536B GLU* 4.8 15.0 + - - +
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Residues in contact with LYS 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A GLU* 2.9 42.3 + - + +
508A GLN* 3.1 46.9 + - + +
509A GLY* 3.4 5.4 + - - +
511A LYS* 1.3 78.0 - - - +
513A HIS* 1.3 66.9 + - - +
514A ASN* 4.8 4.1 + - - -
437B SER 4.4 6.7 + - - -
439B PRO* 4.8 17.4 - - - +
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Residues in contact with HIS 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A GLU* 3.2 45.5 + - + -
484A PHE* 5.1 0.4 - - + -
485A GLU* 3.6 46.1 + - + +
488A MET* 4.2 20.5 - - - +
509A GLY 3.3 11.3 + - - -
510A ALA 3.4 2.0 + - - -
511A LYS 3.0 0.6 - - - -
512A LYS* 1.3 80.7 - - + +
514A ASN* 1.3 77.9 + - - +
515A MET* 3.2 32.4 + - + +
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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