Contacts of the helix formed by residues 679 - 688 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484B THR* 5.8 2.7 - - - +
535B TYR* 3.8 3.6 - - - -
553B LYS* 3.5 42.6 - - - +
557B ASP* 2.8 39.4 + - - -
561B THR* 4.5 11.0 - - + -
582B LEU* 6.4 2.0 - - - -
676B ARG 4.2 3.4 + - - -
678B PRO* 1.3 82.2 - - + +
680B LEU* 1.3 59.5 + - - +
681B ARG 3.3 2.9 - - - -
682B GLN* 3.3 44.6 + - + +
683B CYS* 3.0 34.4 + - - -
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Residues in contact with LEU 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B ASN* 4.6 11.9 - - + +
662B ARG* 3.7 37.7 - - + +
676B ARG* 4.0 13.0 + - + +
677B GLY* 3.6 32.3 - - - +
678B PRO 4.3 0.4 - - - -
679B ARG* 1.3 73.3 - - - +
681B ARG* 1.3 56.5 + - - +
683B CYS* 3.4 7.1 + - + +
684B ALA* 2.8 35.2 + - - +
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Residues in contact with ARG 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B GLU* 2.7 50.7 + - - +
680B LEU* 1.3 77.2 - - - +
682B GLN* 1.3 88.6 + - - +
684B ALA* 3.4 8.4 + - + +
685B PHE* 3.2 19.6 + - - +
813B SO4 5.1 15.4 + - - -
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Residues in contact with GLN 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B GLU* 3.7 18.1 + - - +
535B TYR* 3.7 12.4 + - + +
557B ASP* 3.4 18.4 - - - +
562B CYS* 4.3 0.9 - - - -
679B ARG* 3.3 55.8 + - + +
681B ARG* 1.3 111.2 + - - +
683B CYS* 1.3 58.4 - - - +
684B ALA 3.5 0.2 - - - -
685B PHE* 3.3 12.1 - - - +
686B TRP* 3.2 23.6 - - - -
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Residues in contact with CYS 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561B THR* 4.4 2.0 - - - -
562B CYS* 2.0 61.0 - - + +
565B ASN* 4.0 17.9 - - + +
678B PRO 4.3 1.6 - - - -
679B ARG* 3.0 24.2 + - - +
680B LEU* 3.9 8.7 - - + +
682B GLN* 1.3 75.8 - - - +
684B ALA* 1.3 57.9 + - - +
685B PHE 3.2 1.6 - - - -
686B TRP* 3.5 2.2 + - - +
687B LYS* 3.1 33.3 + - - +
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Residues in contact with ALA 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680B LEU 2.8 19.1 + - - +
681B ARG* 3.7 8.1 - - - +
683B CYS* 1.3 72.4 - - - +
685B PHE* 1.3 59.2 - - - +
688B LYS* 3.0 27.7 + - + +
689B TYR* 3.0 25.4 + - - +
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Residues in contact with PHE 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530B ALA* 3.3 46.0 - - + -
531B ILE* 3.6 21.3 - - + -
533B PHE* 6.0 0.9 - + - -
534B GLU* 3.7 32.5 - - + -
535B TYR* 4.3 1.1 - + - -
681B ARG 3.2 12.3 + - - +
682B GLN 3.3 12.1 - - - +
683B CYS 3.2 0.4 - - - -
684B ALA* 1.3 77.1 - - - +
686B TRP* 1.3 92.8 + + - +
689B TYR* 4.0 24.5 - + - -
690B LEU* 2.8 49.9 + - + +
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Residues in contact with TRP 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520B ASN* 3.9 17.0 - - - -
523B VAL* 6.1 0.7 - - + -
531B ILE* 3.8 28.9 - - + -
535B TYR* 2.8 36.0 + + - -
554B MET* 3.7 16.5 + - + -
557B ASP* 3.9 15.9 - - + +
558B TYR* 3.4 47.8 - + + +
562B CYS* 4.4 8.3 - - + -
682B GLN 3.2 22.0 + - - -
683B CYS* 3.5 6.1 + - - +
684B ALA 3.5 0.2 - - - -
685B PHE* 1.3 91.3 - + - +
687B LYS* 1.3 58.2 + - + +
690B LEU* 3.5 31.5 - - + +
691B PRO* 3.3 19.1 - - - +
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Residues in contact with LYS 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562B CYS* 5.9 4.9 - - + +
566B GLU* 3.6 42.6 + - + +
683B CYS* 3.1 17.2 + - + +
684B ALA* 5.1 0.2 - - - -
686B TRP* 1.3 77.5 - - + +
688B LYS* 1.3 90.0 + - + +
691B PRO* 3.5 14.2 - - + +
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Residues in contact with LYS 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B GLU* 6.3 0.2 - - - +
684B ALA* 3.0 26.3 + - + +
687B LYS* 1.3 114.0 - - + +
689B TYR* 1.3 63.9 + - - +
690B LEU 3.7 0.2 - - - -
691B PRO* 3.8 6.2 - - - +
692B GLN* 3.5 24.0 + - - +
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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