Contacts of the helix formed by residues 679 - 688 (chain A) in PDB entry 5YDJ
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 ARG 679 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A THR* 5.8 3.4 - - - +
535A TYR* 3.9 3.2 - - - -
553A LYS* 3.2 38.4 - - - +
557A ASP* 2.8 40.2 + - - +
561A THR* 4.7 10.5 - - + -
582A LEU* 6.2 2.9 - - - -
676A ARG 4.6 2.6 + - - -
677A GLY* 4.1 1.0 - - - -
678A PRO* 1.3 79.5 - - + +
680A LEU* 1.3 62.2 + - - +
681A ARG 3.4 2.7 - - - -
682A GLN* 3.4 45.9 + - + +
683A CYS* 3.1 29.9 + - - -
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Residues in contact with LEU 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A ASN* 4.7 12.8 - - + +
569A GLN* 6.4 0.2 - - + -
657A HIS* 6.2 0.4 - - + -
662A ARG* 3.7 38.1 - - + +
676A ARG* 3.8 15.6 + - + +
677A GLY* 3.6 31.6 - - - +
679A ARG* 1.3 73.4 - - - +
681A ARG* 1.3 59.7 + - - +
683A CYS* 3.8 5.5 - - + +
684A ALA* 2.8 30.5 + - - +
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Residues in contact with ARG 681 (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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533A PHE* 6.3 0.6 - - - -
534A GLU* 3.1 39.6 + - - +
679A ARG 3.4 0.6 - - - -
680A LEU* 1.3 76.0 - - - +
682A GLN* 1.3 81.4 + - - +
684A ALA* 3.4 8.1 + - + +
685A PHE* 3.0 25.8 + - - +
809A SO4 4.4 16.4 + - - -
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Residues in contact with GLN 682 (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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534A GLU* 3.7 21.5 + - + +
535A TYR* 3.6 11.3 + - + +
557A ASP* 3.4 20.0 - - - +
679A ARG* 3.4 62.6 - - - +
681A ARG* 1.3 99.2 + - - +
683A CYS* 1.3 59.5 + - - +
685A PHE* 3.3 15.4 - - - +
686A TRP* 3.1 23.9 + - - -
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Residues in contact with CYS 683 (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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561A THR* 4.5 1.8 - - - -
562A CYS* 2.0 60.6 - - + +
565A ASN* 3.8 17.5 - - + +
678A PRO 4.3 1.6 - - - -
679A ARG* 3.1 26.6 + - - +
680A LEU* 3.9 8.1 - - + +
682A GLN* 1.3 74.8 - - - +
684A ALA* 1.3 58.2 + - - +
685A PHE 3.2 0.2 - - - -
686A TRP* 3.8 1.1 - - - +
687A LYS* 2.9 38.9 + - + +
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Residues in contact with ALA 684 (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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680A LEU 2.8 23.0 + - - +
681A ARG* 3.5 9.9 - - + +
683A CYS* 1.3 69.3 - - - +
685A PHE* 1.3 61.0 + - - +
687A LYS* 5.1 0.4 - - - -
688A LYS* 3.0 37.3 + - + +
689A TYR* 3.1 10.1 + - - +
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Residues in contact with PHE 685 (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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530A ALA* 3.6 39.3 - - + -
531A ILE* 3.8 18.8 - - + -
534A GLU* 3.7 29.2 - - + +
535A TYR* 4.0 8.7 - + - -
681A ARG 3.0 14.0 + - - +
682A GLN 3.3 10.5 - - - +
683A CYS 3.2 0.2 - - - -
684A ALA* 1.3 75.0 - - - +
686A TRP* 1.3 102.2 + + - +
689A TYR* 3.3 28.1 + + - -
690A LEU* 2.9 44.1 + - + +
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Residues in contact with TRP 686 (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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520A ASN* 4.0 27.6 - - - -
531A ILE* 4.1 8.1 - - + -
535A TYR* 2.6 31.2 + + - -
554A MET* 3.6 21.8 - - + -
557A ASP* 3.6 18.9 - - + +
558A TYR* 3.4 49.0 - + + +
562A CYS* 4.3 6.1 - - + -
682A GLN 3.1 20.3 + - - -
683A CYS* 3.3 6.8 + - - +
685A PHE* 1.3 96.3 - + - +
687A LYS* 1.3 69.7 + - + +
690A LEU* 3.4 31.7 - - + +
691A PRO* 3.2 19.9 - - - +
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Residues in contact with LYS 687 (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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390A THR* 4.1 8.9 + - - -
558A TYR* 6.5 1.1 - - + -
562A CYS* 4.6 17.7 - - + +
563A ASN* 3.7 20.4 + - - +
566A GLU* 2.8 38.4 + - + -
683A CYS* 2.9 26.6 + - + +
684A ALA* 5.1 0.2 - - - -
686A TRP* 1.3 83.3 - - + +
688A LYS* 1.3 77.4 + - + +
691A PRO* 3.6 12.7 - - - +
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Residues in contact with LYS 688 (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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684A ALA* 3.0 23.0 + - + +
686A TRP 3.6 0.2 - - - -
687A LYS* 1.3 93.1 + - + +
689A TYR* 1.3 66.8 + - + +
691A PRO* 3.7 7.7 - - - +
692A GLN* 3.6 20.6 + - - +
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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