Contacts of the helix formed by residues 513 - 525 (chain A) in PDB entry 1HS6
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 PRO 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476A ILE 6.1 0.9 - - - +
511A PRO 4.7 1.1 - - - +
512A LEU* 1.3 91.4 - - + +
514A LEU* 1.3 67.0 + - - +
515A GLY 4.4 2.2 - - - +
516A HIS* 2.8 53.7 + - + +
517A ILE* 3.2 8.8 + - - +
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Residues in contact with LEU 514 (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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512A LEU 3.2 3.2 + - - -
513A PRO* 1.3 71.4 - - - +
515A GLY* 1.3 63.1 + - - +
517A ILE* 3.0 7.8 + - + +
518A LYS* 2.9 45.3 + - + +
545A SER 3.8 14.0 + - - +
546A LYS* 4.2 11.2 - - + +
547A TRP* 3.5 49.8 - - + +
548A GLU 5.8 0.2 - - - +
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Residues in contact with GLY 515 (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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483A LEU* 4.8 5.9 - - - +
513A PRO* 3.2 3.2 - - - +
514A LEU* 1.3 77.7 - - - +
516A HIS* 1.3 67.0 + - - +
518A LYS* 3.4 11.5 + - - +
519A ARG* 3.0 23.2 + - - +
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Residues in contact with HIS 516 (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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475A TRP* 3.3 34.5 - + + -
476A ILE 5.9 0.2 - - - -
478A ALA* 3.2 43.6 + - + +
479A LYS* 4.9 5.2 - - - -
480A GLU* 5.1 3.1 - - + -
483A LEU* 3.7 28.3 - - + +
512A LEU* 4.6 8.3 - - + -
513A PRO* 2.8 46.1 + - + +
515A GLY* 1.3 77.5 - - - +
517A ILE* 1.3 62.5 + - - +
519A ARG 3.2 1.0 + - - -
520A MET* 2.8 24.3 + - - +
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Residues in contact with ILE 517 (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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512A LEU* 3.6 27.8 - - + -
513A PRO 3.7 8.5 - - - +
514A LEU* 3.0 8.9 + - + +
516A HIS* 1.3 74.4 - - - +
518A LYS* 1.3 67.9 + - - +
520A MET* 3.1 12.7 + - + +
521A GLN* 3.0 19.1 + - - +
538A TRP* 3.8 7.9 - - + -
541A LEU* 3.8 27.6 - - + -
542A CYS* 3.8 38.4 - - - +
545A SER* 3.5 25.8 - - - +
547A TRP* 3.8 11.2 - - + -
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Residues in contact with LYS 518 (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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514A LEU* 2.9 38.6 + - + +
515A GLY* 3.6 11.2 - - - +
517A ILE* 1.3 77.6 - - - +
519A ARG* 1.3 62.8 + - - +
521A GLN* 3.1 5.0 + - - +
522A GLU* 3.0 23.2 + - - +
547A TRP* 3.2 53.6 - - + +
549A ASP* 4.5 4.4 + - - -
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Residues in contact with ARG 519 (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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475A TRP* 3.9 14.4 - - + -
483A LEU* 2.7 43.8 + - + +
484A ASN* 3.2 33.7 + - - +
486A PHE 3.4 11.3 + - - -
515A GLY 3.0 14.0 + - - +
516A HIS 3.5 8.5 - - - +
518A LYS* 1.3 76.0 - - - +
520A MET* 1.3 58.4 + - - +
522A GLU* 2.8 45.3 + - - +
523A VAL* 2.8 49.1 + - + +
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Residues in contact with MET 520 (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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475A TRP* 3.4 53.1 - - + -
502A PHE* 4.2 11.4 - - + -
506A THR* 4.6 2.0 - - + -
512A LEU* 4.6 4.7 - - + -
516A HIS 2.8 11.0 + - - +
517A ILE* 3.4 24.2 - - + +
518A LYS 3.1 0.2 - - - -
519A ARG* 1.3 78.6 - - - +
521A GLN* 1.3 62.1 + - - +
523A VAL* 3.9 0.8 - - - +
524A TYR* 2.9 41.7 + - + +
526A PHE* 4.0 14.2 - - + -
538A TRP* 3.7 24.0 - - + -
541A LEU* 4.1 15.0 - - + -
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Residues in contact with GLN 521 (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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517A ILE 3.0 6.7 + - - -
518A LYS 3.1 3.1 + - - +
520A MET* 1.3 76.6 - - - +
522A GLU* 1.3 61.6 + - - +
525A ASN* 2.8 48.6 + - - +
526A PHE 3.0 14.3 - - - +
527A ASN* 2.9 53.8 - - - +
538A TRP* 3.6 14.6 - - + -
547A TRP* 3.6 28.7 - - + -
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Residues in contact with GLU 522 (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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518A LYS 3.0 12.5 + - - +
519A ARG* 2.8 48.5 + - - +
521A GLN* 1.3 81.7 - - - +
523A VAL* 1.3 60.0 + - - +
525A ASN* 4.7 1.4 + - - +
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Residues in contact with VAL 523 (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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475A TRP* 4.0 17.7 - - + -
486A PHE* 3.6 14.1 - - + +
487A ASN* 4.1 12.6 - - - +
488A ALA* 3.5 25.2 - - - +
519A ARG* 2.8 66.4 + - - +
520A MET 3.9 3.4 - - - +
522A GLU* 1.3 76.2 - - - +
524A TYR* 1.3 80.1 + - + +
525A ASN* 3.7 0.4 - - - -
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Residues in contact with TYR 524 (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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471A LEU* 3.7 5.0 - - + +
475A TRP* 2.9 44.4 + + - -
487A ASN 3.2 22.9 - - - -
488A ALA* 4.2 1.6 - - - +
490A ASP* 2.6 31.1 + - + +
491A LEU* 3.5 38.5 - - + +
502A PHE* 4.3 9.2 - + - -
520A MET* 2.9 21.7 + - + +
523A VAL* 1.3 91.3 - - + +
525A ASN* 1.3 73.4 + - - +
526A PHE* 3.2 37.7 + + + -
529A ILE* 5.1 2.3 - - - +
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Residues in contact with ASN 525 (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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521A GLN* 2.8 37.8 + - - +
522A GLU 5.6 1.1 - - - +
523A VAL 3.7 0.8 - - - -
524A TYR* 1.3 80.0 - - - +
526A PHE* 1.3 64.0 + - - +
527A ASN* 3.1 4.6 - - - +
528A ALA* 3.3 36.8 + - - +
529A ILE* 4.1 6.1 + - - +
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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