Contacts of the helix formed by residues 704 - 713 (chain X) in PDB entry 6AH0
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 GLU 704 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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703X ARG* 1.3 72.3 - - - +
705X PHE* 1.3 62.1 + - - +
707X LEU* 3.2 12.4 + - - +
708X SER* 3.2 11.3 + - - -
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Residues in contact with PHE 705 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703X ARG 3.0 6.5 - - - +
704X GLU* 1.3 78.3 - - - +
706X ALA* 1.3 62.0 + - - +
708X SER* 3.6 1.3 + - - +
709X ASN* 3.5 15.4 + - - -
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Residues in contact with ALA 706 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692X CYS* 6.3 3.4 - - - +
703X ARG* 3.2 11.9 + - - +
704X GLU 3.2 1.0 - - - -
705X PHE* 1.3 78.7 - - - +
707X LEU* 1.3 60.4 + - - +
708X SER 3.5 0.2 + - - -
709X ASN* 3.6 1.6 + - - -
710X LEU* 3.2 18.0 + - - -
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Residues in contact with LEU 707 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703X ARG 3.7 5.6 + - - -
704X GLU* 3.2 7.0 + - - +
706X ALA* 1.3 73.4 - - - +
708X SER* 1.3 56.8 + - - +
710X LEU* 4.5 2.0 - - - +
711X LYS* 2.7 32.6 + - - -
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Residues in contact with SER 708 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704X GLU 3.2 13.1 + - - -
705X PHE* 3.6 2.7 + - - +
706X ALA 3.3 0.4 - - - -
707X LEU* 1.3 76.1 - - - +
709X ASN* 1.3 50.9 + - - +
711X LYS* 3.1 2.8 + - - +
712X ALA* 2.6 35.0 + - - -
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Residues in contact with ASN 709 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705X PHE 3.5 11.3 + - - -
706X ALA 4.0 2.7 - - - -
707X LEU 3.4 0.4 - - - -
708X SER* 1.3 74.4 - - - +
710X LEU* 1.3 51.8 + - - +
712X ALA* 3.5 1.3 - - - +
713X GLY 2.7 31.2 + - - -
714X ALA* 2.8 13.6 + - - +
715X LYS 3.8 11.2 - - - +
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Residues in contact with LEU 710 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665X PRO 5.8 0.7 - - - -
666X PRO* 5.6 7.5 - - - +
706X ALA 3.2 14.1 + - - -
707X LEU* 3.8 3.4 - - - +
708X SER 3.3 0.2 - - - -
709X ASN* 1.3 73.4 - - - +
711X LYS* 1.3 63.6 + - - +
713X GLY* 3.0 13.9 + - - -
715X LYS* 3.4 20.7 + - - +
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Residues in contact with LYS 711 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707X LEU 2.7 21.0 + - - -
708X SER 3.4 1.6 - - - -
710X LEU* 1.3 73.6 - - - +
712X ALA* 1.3 60.1 + - - +
713X GLY 3.5 0.2 + - - -
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Residues in contact with ALA 712 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708X SER 2.6 19.7 + - - -
709X ASN* 3.5 2.7 - - - +
711X LYS* 1.3 74.4 - - - +
713X GLY* 1.3 57.2 + - - +
714X ALA 3.4 4.4 + - - +
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Residues in contact with GLY 713 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665X PRO* 6.1 4.3 - - - -
709X ASN 2.7 8.1 + - - -
710X LEU 3.0 10.8 + - - -
711X LYS 3.3 0.8 + - - -
712X ALA* 1.3 74.5 - - - +
714X ALA* 1.3 67.9 + - - +
715X LYS 3.5 6.5 + - - +
716X ASP* 5.2 1.2 - - - -
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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