Contacts of the helix formed by residues 704 - 712 (chain A) in PDB entry 2DFS
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 TYR 704 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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703A THR* 1.3 74.9 - - - +
705A GLN* 1.4 56.7 + - - +
707A PHE* 4.5 2.5 - - - -
708A PHE* 3.1 30.8 + - - +
724A ARG* 5.1 2.8 - - + +
725A LYS* 3.5 61.5 - - + +
728A CYS* 3.6 24.0 - - + -
729A LYS* 5.9 1.1 - - + -
744A PHE* 3.5 21.8 - + - -
745A GLY 3.0 17.9 + - - -
746A LYS 4.5 0.2 - - - -
747A THR* 3.3 32.3 - - - -
748A LYS 2.8 23.4 + - - -
749A ILE* 3.5 17.3 - - + -
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Residues in contact with GLN 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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703A THR* 3.2 9.9 + - - +
704A TYR* 1.4 76.0 - - - +
706A GLU* 1.4 72.3 + - + +
708A PHE* 3.6 2.3 + - - +
709A SER* 2.9 43.4 + - - -
724A ARG* 2.7 48.9 + - - +
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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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702A TRP* 3.7 26.4 - - + -
703A THR* 2.6 59.2 + - - +
705A GLN* 1.4 83.4 - - + +
707A PHE* 1.4 66.3 + - - +
709A SER* 3.3 15.7 + - - -
710A ARG* 3.3 11.1 + - - +
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Residues in contact with PHE 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A TRP* 3.6 15.6 - + + -
703A THR 3.1 15.8 + - - +
704A TYR 4.0 3.1 - - - +
706A GLU* 1.4 77.6 - - - +
708A PHE* 1.3 63.1 + - - +
711A TYR* 3.1 54.4 + + + +
715A MET* 5.1 2.5 - - + -
728A CYS* 3.7 38.8 - - + -
731A VAL* 4.9 11.9 - - + -
732A LEU* 3.9 27.8 - - + -
735A LEU* 5.7 1.8 - - + -
749A ILE* 3.7 18.2 - - + -
751A PHE* 3.7 26.9 - + - -
759A LEU* 3.7 19.1 - - + -
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Residues in contact with PHE 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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704A TYR 3.1 20.1 + - - +
705A GLN 3.7 0.4 - - - +
707A PHE* 1.3 77.1 - - - +
709A SER* 1.3 57.4 + - - +
712A ARG* 3.0 51.8 + - + +
715A MET* 4.2 17.9 - - + -
720A VAL* 4.4 12.6 - - + -
721A LEU 5.4 0.9 - - - -
724A ARG* 3.2 76.5 - - + +
727A THR* 4.1 17.3 - - + -
728A CYS* 4.0 8.3 - - - -
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Residues in contact with SER 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 GLN* 2.9 32.3 + - - -
706A GLU* 3.3 10.4 + - - -
708A PHE* 1.3 82.3 - - - +
710A ARG* 1.3 61.0 + - - +
712A ARG* 4.0 9.0 + - - +
713A VAL* 6.0 0.2 - - - +
724A ARG* 4.6 2.3 + - - -
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Residues in contact with ARG 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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67A ILE* 3.5 44.8 - - - +
702A TRP* 4.1 9.9 - - + -
706A GLU 3.3 11.7 + - - +
709A SER* 1.3 79.0 - - - +
711A TYR* 1.4 77.5 + - + +
712A ARG 3.6 0.4 - - - -
713A VAL* 3.8 11.1 - - - +
760A GLU* 2.7 45.9 + - - +
763A ARG* 3.2 38.5 + - - +
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Residues in contact with TYR 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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702A TRP* 3.9 29.7 - + - -
707A PHE* 3.1 53.4 + + + +
708A PHE 3.8 2.0 - - - -
710A ARG* 1.4 84.8 - - + +
712A ARG* 1.4 56.5 + - - +
713A VAL 3.2 3.1 - - - -
714A LEU* 2.9 48.4 + - + +
715A MET* 3.5 14.7 - - + +
731A VAL* 5.4 1.3 - - + +
735A LEU* 5.8 2.2 - - + -
756A VAL* 4.2 5.2 - - - +
759A LEU* 3.8 40.1 - - + +
760A GLU* 2.7 38.8 + - - +
763A ARG* 3.7 9.6 - - - -
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Residues in contact with ARG 712 (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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708A PHE* 3.0 40.3 + - + +
709A SER* 4.2 7.9 - - - +
710A ARG 3.6 2.2 - - - -
711A TYR* 1.4 75.1 - - - +
713A VAL* 1.3 59.8 - - + +
715A MET* 3.5 37.3 + - - +
717A GLN* 2.9 39.8 + - - +
720A VAL* 3.6 26.4 - - - +
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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