Contacts of the helix formed by residues 514 - 525 (chain A) in PDB entry 3A1B
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 CYS 514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ZN 2.3 36.1 - - - -
494A CYS* 3.3 11.2 - - + +
497A CYS* 3.8 6.1 - - - -
499A SER* 4.1 14.6 - - - +
501A ASN* 3.4 23.8 - - + +
503A THR* 4.2 0.4 - - - -
504A LEU* 3.9 2.0 - - - -
513A MET* 1.3 78.7 - - - +
515A GLN* 1.3 61.6 + - - +
516A ASN* 3.9 12.1 - - - +
517A CYS* 3.2 17.8 + - - -
518A LYS* 2.9 24.8 + - - +
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Residues in contact with GLN 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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501A ASN* 4.7 2.0 + - - +
503A THR* 3.4 21.7 + - + +
504A LEU* 4.3 7.1 - - - +
514A CYS* 1.3 73.4 - - - +
516A ASN* 1.3 57.1 + - - +
518A LYS* 3.1 27.6 + - - +
519A ASN* 2.9 58.8 + - - +
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Residues in contact with ASN 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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497A CYS* 5.4 3.2 - - - +
514A CYS* 3.3 10.1 - - - -
515A GLN* 1.3 77.4 - - - +
517A CYS* 1.3 73.8 + - - +
519A ASN* 3.4 12.0 + - - +
520A CYS* 3.1 32.3 + - - -
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Residues in contact with CYS 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ZN 2.4 34.5 - - - -
494A CYS* 3.9 5.8 - - - -
496A SER* 3.1 31.0 - - - +
497A CYS* 3.7 11.0 - - - -
513A MET* 3.8 8.7 - - + +
514A CYS* 3.2 8.4 + - - +
516A ASN* 1.3 84.3 - - - +
518A LYS* 1.3 67.6 + - - +
520A CYS* 3.1 9.2 + - - +
521A PHE* 2.9 23.9 + - - +
540A CYS 5.8 0.4 - - - -
541A CYS* 4.6 1.7 - - - -
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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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504A LEU* 4.2 20.6 - - + +
513A MET* 4.0 5.7 - - - +
514A CYS 2.9 13.3 + - - +
515A GLN* 3.1 29.1 + - - +
517A CYS* 1.3 77.3 - - - +
519A ASN* 1.3 65.0 + - - +
521A PHE* 3.1 2.8 + - - +
522A LEU* 3.0 37.9 + - + +
607A MET 5.5 0.6 + - - -
608A PHE* 3.4 62.5 + - + +
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Residues in contact with ASN 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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515A GLN* 2.9 42.6 + - - +
516A ASN* 3.6 13.6 - - - +
517A CYS 3.2 0.2 - - - -
518A LYS* 1.3 76.2 - - - +
520A CYS* 1.3 60.7 + - - +
522A LEU* 3.5 18.0 + - - +
523A GLU* 3.4 35.0 + - - +
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Residues in contact with CYS 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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516A ASN* 3.1 32.5 + - - -
517A CYS* 3.1 10.3 + - - +
519A ASN* 1.3 71.8 - - - +
521A PHE* 1.3 56.3 + - - +
523A GLU* 3.1 9.6 + - - +
524A CYS* 2.7 41.4 + - - +
541A CYS* 4.0 20.9 - - + -
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Residues in contact with PHE 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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7A EDO 3.2 26.2 - - - -
506A HIS* 4.2 10.8 - + - -
507A PRO* 4.3 6.1 - - + -
508A LEU* 4.1 18.6 - - + -
513A MET* 3.9 18.6 - - + -
517A CYS 2.9 13.0 + - - +
518A LYS 3.4 9.4 - - - +
520A CYS* 1.3 76.1 - - - +
522A LEU* 1.3 61.6 + - - +
524A CYS* 4.5 0.7 - - - +
525A ALA* 3.0 27.2 + - - +
538A THR 3.2 25.8 - - - -
539A ILE 5.3 0.2 - - - -
541A CYS* 3.6 16.1 - - - -
605A LEU* 4.0 9.9 - - + -
608A PHE* 3.3 24.5 - + + -
609A PHE* 3.9 19.3 - + - -
615A EDO 3.7 14.3 - - - -
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Residues in contact with LEU 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 37.6 + - + +
519A ASN* 3.7 19.5 - - - +
520A CYS 3.2 0.2 - - - -
521A PHE* 1.3 77.8 - - - +
523A GLU* 1.3 61.0 + - + +
525A ALA* 3.9 0.5 - - - +
526A TYR* 3.2 27.9 - - + -
608A PHE* 3.7 31.2 - - + +
609A PHE* 3.7 32.5 - - + +
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Residues in contact with GLU 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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5A EDO 3.2 32.2 - - - +
519A ASN* 3.4 25.1 + - - +
520A CYS* 3.1 10.5 + - - +
522A LEU* 1.3 78.0 - - + +
524A CYS* 1.3 67.1 + - - +
526A TYR* 3.1 13.0 + - - +
527A GLN* 3.7 5.0 + - - +
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Residues in contact with CYS 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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464A LYS* 4.5 4.3 - - - -
520A CYS* 2.7 25.9 + - - +
523A GLU* 1.3 74.8 - - - +
525A ALA* 1.3 63.1 + - - +
526A TYR 3.1 1.0 + - - -
527A GLN* 3.1 41.9 + - - +
534A GLN* 4.6 3.3 - - - +
535A SER 5.4 0.3 + - - -
536A TYR* 4.0 9.7 + - + -
541A CYS* 3.6 29.6 - - + -
615A EDO 3.4 31.7 + - - +
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Residues in contact with ALA 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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7A EDO 3.5 23.6 - - - -
521A PHE 3.0 18.3 + - - +
522A LEU 3.9 3.1 - - - +
523A GLU 3.2 0.6 + - - -
524A CYS* 1.3 76.6 - - - +
526A TYR* 1.3 56.0 + - + +
527A GLN 3.4 0.7 - - - -
528A TYR* 3.3 13.2 - - - -
534A GLN* 3.5 4.2 - - - +
609A PHE* 3.5 32.3 - - + -
615A EDO 3.8 2.2 - - - -
617A EDO 2.3 31.3 + - - +
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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