Contacts of the helix formed by residues 704 - 711 (chain A) in PDB entry 5Y36
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 PHE 704 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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666A LEU* 4.4 15.3 - - + -
670A ILE* 3.4 52.9 - - + -
671A ARG 4.4 0.4 - - - -
672A ASP* 4.1 30.7 - - + -
677A LYS 4.3 5.6 - - - -
679A ILE* 4.4 23.1 - - + -
682A PHE* 4.9 3.4 - + - -
697A ILE* 4.3 26.8 - - + +
702A LEU* 3.2 30.5 - - + -
703A THR* 1.3 79.0 - - - +
705A LYS* 1.4 62.4 + - - +
706A GLU 3.3 1.3 - - - -
707A ASP* 3.3 24.8 + - + +
708A ILE* 3.4 14.6 + - - +
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Residues in contact with LYS 705 (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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697A ILE 4.7 2.5 + - - +
698A HIS 5.1 5.8 - - - +
699A ASP 5.4 4.0 + - - +
700A ASP* 3.0 37.4 + - - +
702A LEU 4.0 11.3 + - - +
703A THR* 3.2 1.3 - - - -
704A PHE* 1.4 75.7 - - - +
706A GLU* 1.4 57.9 + - - +
708A ILE* 3.3 19.6 + - + +
709A GLN* 3.0 47.3 + - + +
947A ASP* 2.9 32.2 + - - -
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Residues in contact with GLU 706 (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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673A LYS* 2.8 38.6 + - - +
703A THR 3.7 11.8 + - - +
705A LYS* 1.4 78.1 - - - +
707A ASP* 1.3 58.3 + - - +
709A GLN* 3.2 18.4 + - + +
710A LYS* 3.0 63.1 + - + +
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Residues in contact with ASP 707 (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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670A ILE* 3.4 38.2 - - + +
703A THR 5.3 1.6 - - - -
704A PHE* 3.3 21.3 + - + +
706A GLU* 1.3 78.9 - - - +
708A ILE* 1.4 56.3 + - + +
710A LYS* 3.5 14.1 + - - +
711A ALA* 3.0 34.1 + - - +
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Residues in contact with ILE 708 (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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697A ILE* 3.7 37.5 - - + +
698A HIS* 3.9 26.7 - - + +
704A PHE 3.4 9.8 + - - +
705A LYS* 3.3 19.2 + - + +
707A ASP* 1.4 75.9 - - + +
709A GLN* 1.4 58.9 + - + +
711A ALA* 4.9 1.1 - - - -
712A GLN* 2.9 58.6 + - + +
713A VAL* 3.1 19.1 + - + -
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Residues in contact with GLN 709 (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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705A LYS* 3.0 37.3 + - + +
706A GLU* 3.2 21.3 + - - +
708A ILE* 1.4 75.6 - - + +
710A LYS* 1.3 60.4 + - + +
713A VAL* 3.5 33.4 - - + +
714A SER* 3.8 8.3 + - - -
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Residues in contact with LYS 710 (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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706A GLU* 3.0 53.2 + - + +
707A ASP* 3.9 11.7 + - - +
709A GLN* 1.3 76.1 - - + +
711A ALA* 1.3 60.8 + - - +
714A SER* 4.0 11.4 - - - -
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Residues in contact with ALA 711 (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 4.6 15.3 - - - +
502A LEU* 6.5 0.4 - - + -
503A PRO* 5.5 8.1 - - + -
707A ASP 3.0 18.2 + - - +
708A ILE* 4.9 0.2 - - - -
710A LYS* 1.3 75.4 - - + +
712A GLN* 1.3 69.9 + - + +
713A VAL 3.6 0.7 - - - -
714A SER* 3.5 17.8 - - - -
715A GLY 4.1 2.6 + - - -
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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