Contacts of the helix formed by residues 512 - 521 (chain A) in PDB entry 4YK6
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 ASP 512 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467A ASN* 3.7 13.2 + - - -
508A LEU 3.5 18.3 - - - +
509A THR 3.1 5.8 + - - +
510A PHE 3.1 5.7 - - - +
511A GLY* 1.3 77.8 - - - +
513A VAL* 1.3 63.7 + - - +
514A ALA* 3.3 9.7 + - - +
515A ASN* 2.8 44.0 + - - +
516A LYS* 3.1 28.0 + - - +
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Residues in contact with VAL 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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511A GLY 3.9 5.5 + - - +
512A ASP* 1.3 72.3 + - - +
514A ALA* 1.3 65.3 + - - +
516A LYS* 3.4 10.7 + - + +
517A ALA* 3.2 22.4 + - + +
554A ARG* 6.1 7.9 - - + +
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Residues in contact with ALA 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 ASP* 3.3 7.6 + - - +
513A VAL* 1.3 81.0 - - - +
515A ASN* 1.3 61.0 - - - +
517A ALA* 3.3 7.8 + - - +
518A THR* 3.0 33.1 + - - +
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Residues in contact with ASN 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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467A ASN* 2.9 38.7 + - - +
472A LEU* 3.5 26.2 - - + +
508A LEU* 2.9 37.6 + - - +
509A THR* 4.3 3.4 - - - +
512A ASP* 2.8 20.4 + - - +
514A ALA* 1.3 78.8 - - - +
516A LYS* 1.3 60.4 + - - +
518A THR* 3.4 3.3 + - - -
519A LEU* 2.9 30.5 + - - +
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Residues in contact with LYS 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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509A THR* 3.1 32.1 - - - +
511A GLY* 5.1 0.8 - - - -
512A ASP 3.1 19.6 + - - +
513A VAL* 3.6 10.3 - - + +
515A ASN* 1.3 75.6 - - - +
517A ALA* 1.3 63.0 + - - +
520A CYS* 3.0 30.6 + - - +
550A ASN* 3.0 29.4 + - - +
551A LEU* 3.7 22.3 - - + +
553A TRP* 3.1 31.8 + - - +
554A ARG* 4.8 5.2 - - + +
555A ALA* 6.2 0.4 - - - -
559A SER* 4.7 3.6 - - - +
370B GLU* 3.1 21.3 + - - -
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Residues in contact with ALA 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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513A VAL* 3.2 11.5 + - + +
514A ALA* 3.5 10.8 - - - +
516A LYS* 1.3 79.8 - - - +
518A THR* 1.3 62.1 + - - +
520A CYS* 3.5 2.3 + - - +
521A SER* 3.1 23.6 + - - -
556A ASP* 4.2 17.5 - - - +
559A SER* 4.3 10.5 - - - -
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Residues in contact with THR 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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472A LEU* 3.8 19.1 - - + -
473A GLN* 3.8 31.9 - - + +
514A ALA* 3.0 19.3 + - - +
515A ASN* 3.7 7.2 + - - -
517A ALA* 1.3 77.4 - - - +
519A LEU* 1.3 63.8 - - - +
521A SER* 2.7 27.7 + - - +
522A MET* 3.4 9.7 - - + +
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Residues in contact with LEU 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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472A LEU* 4.1 7.8 - - + +
476A ALA* 3.8 29.6 - - + -
505A LEU* 4.3 18.8 - - + -
509A THR* 4.0 11.4 - - + -
515A ASN 2.9 17.3 + - - +
516A LYS 4.0 2.9 - - - +
518A THR* 1.3 78.3 - - - +
520A CYS* 1.3 56.1 + - - +
522A MET* 2.9 31.0 + - - +
525A CYS* 4.1 16.2 - - + -
526A MET* 3.7 9.8 - - - +
529A LEU* 4.8 2.7 - - + -
547A VAL* 3.8 29.6 - - + -
551A LEU* 3.8 20.4 - - + -
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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 LYS 3.0 19.6 + - - +
517A ALA 3.9 2.7 - - - +
519A LEU* 1.3 75.9 - - - +
521A SER* 1.3 60.2 + - - +
522A MET 3.1 0.9 + - - -
523A LYS* 3.5 5.8 - - - +
526A MET* 3.8 17.2 - - - +
551A LEU* 4.0 30.1 - - - -
558A ASN 5.5 0.4 - - - -
559A SER* 3.6 45.5 - - - +
562A THR* 3.3 27.4 - - - +
563A LEU* 4.4 2.5 - - - -
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Residues in contact with SER 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 ALA 3.1 13.9 + - - -
518A THR* 2.7 24.2 + - - +
519A LEU 3.2 0.2 - - - -
520A CYS* 1.3 75.3 - - - +
522A MET* 1.3 60.2 + - - +
523A LYS* 3.1 23.2 + - - +
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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