Contacts of the helix formed by residues 686 - 695 (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 GLY 686 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A PHE* 4.8 5.3 - - - -
462A GLN* 4.5 2.0 - - - -
553A PHE* 4.2 20.0 - - - -
554A ALA* 4.9 2.7 - - - -
660A ARG* 4.3 7.0 - - - -
682A LEU 4.2 0.2 - - - -
683A ARG 3.3 11.7 + - - -
684A ALA 3.6 0.8 - - - -
685A CYS* 1.3 76.5 - - - +
687A VAL* 1.4 57.3 + - - +
688A LEU 3.5 2.0 - - - -
689A GLU* 3.6 6.2 + - - +
690A THR* 2.9 36.4 + - - -
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Residues in contact with VAL 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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74A LEU* 5.1 1.1 - - + -
85A VAL* 5.0 3.6 - - + -
89A LEU* 6.1 0.2 - - + -
103A CYS* 4.3 12.3 - - + -
106A VAL* 5.6 2.7 - - + -
108A VAL* 4.9 12.8 - - + -
660A ARG* 4.3 14.8 - - + +
662A ILE* 5.2 0.7 - - + -
682A LEU* 3.3 33.2 + - + +
685A CYS* 3.2 29.6 - - + +
686A GLY* 1.4 78.1 - - - +
688A LEU* 1.3 60.7 + - + +
690A THR* 3.3 4.9 + - - -
691A ILE* 3.0 51.8 + - + +
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Residues in contact with LEU 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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82A GLU* 3.5 47.8 - - + +
85A VAL* 4.0 38.8 - - + -
679A VAL* 4.6 5.4 - - + -
682A LEU* 3.9 29.6 + - + +
683A ARG* 4.1 23.8 - - + +
686A GLY 3.5 0.2 - - - -
687A VAL* 1.3 75.3 - - + +
689A GLU* 1.3 58.0 + - - +
691A ILE* 3.5 9.7 + - + +
692A ARG* 2.9 27.8 + - - +
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Residues in contact with GLU 689 (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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551A LYS* 4.9 3.4 + - - -
553A PHE* 3.4 58.5 - - + +
554A ALA* 4.4 15.6 - - + +
683A ARG* 6.0 0.6 + - - +
686A GLY* 3.6 5.5 + - - +
687A VAL 3.4 0.4 - - - -
688A LEU* 1.3 74.9 - - - +
690A THR* 1.4 63.6 + - - +
692A ARG* 2.6 56.4 + - - +
693A ILE* 3.0 27.0 + - + +
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Residues in contact with THR 690 (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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103A CYS* 5.3 12.8 - - - +
106A VAL* 5.5 3.1 - - + -
462A GLN* 3.7 19.4 + - - -
465A PHE* 3.7 27.8 - - + -
469A VAL* 5.7 4.3 - - + -
553A PHE* 4.3 3.5 - - - -
660A ARG* 5.2 1.6 + - - -
686A GLY 2.9 27.6 + - - -
687A VAL* 3.6 5.8 - - - -
689A GLU* 1.4 69.9 - - - +
691A ILE* 1.3 58.0 + - - +
693A ILE* 3.2 11.7 + - + +
694A SER* 3.0 34.2 + - - +
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Residues in contact with ILE 691 (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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74A LEU* 4.3 4.9 - - + -
75A THR* 6.2 1.8 - - + -
80A LEU* 3.4 40.7 - - + +
81A HIS* 4.9 2.0 - - - +
85A VAL* 3.7 32.8 - - + -
103A CYS* 3.4 30.5 - - - -
687A VAL* 3.0 33.3 + - + +
688A LEU* 3.5 10.1 - - + +
690A THR* 1.3 72.2 - - - +
692A ARG* 1.4 64.0 + - - +
694A SER* 3.2 10.2 + - - +
695A ALA* 3.1 23.7 + - - +
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Residues in contact with ARG 692 (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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80A LEU 5.8 1.1 - - - -
490A TYR* 4.0 25.1 + - - -
688A LEU 2.9 18.3 + - - +
689A GLU* 2.6 48.8 + - - +
691A ILE* 1.4 74.0 - - - +
693A ILE* 1.3 89.5 + - - +
695A ALA* 3.8 10.2 + - - +
696A ALA* 3.9 7.8 + - - +
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Residues in contact with ILE 693 (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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466A ASN* 6.6 0.4 - - - -
488A ASP 4.9 5.2 - - - +
490A TYR* 3.6 46.0 - - + +
553A PHE* 4.9 11.0 - - + -
689A GLU* 3.0 15.6 + - + +
690A THR* 3.2 10.5 + - + +
692A ARG* 1.3 109.9 - - - +
694A SER* 1.3 62.4 + - - +
696A ALA* 3.1 24.2 + - - +
697A GLY 4.1 1.6 + - - -
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Residues in contact with SER 694 (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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75A THR* 5.1 12.7 - - - +
80A LEU* 4.5 10.3 - - - -
103A CYS* 6.1 0.5 - - - -
690A THR* 3.0 22.6 + - - +
691A ILE* 3.2 11.7 + - - +
693A ILE* 1.3 74.8 - - - +
695A ALA* 1.3 60.6 + - - +
696A ALA 3.4 0.9 + - - -
697A GLY* 3.6 10.1 + - - -
698A PHE 4.4 0.3 + - - -
699A PRO* 3.7 21.7 - - - +
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Residues in contact with ALA 695 (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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80A LEU* 4.2 28.9 - - + +
691A ILE 3.1 15.8 + - - +
692A ARG* 4.1 6.7 - - - +
693A ILE 3.2 0.6 + - - -
694A SER* 1.3 73.4 - - - +
696A ALA* 1.4 61.9 + - - +
697A GLY 3.4 4.9 - - - +
699A PRO* 4.2 10.1 - - - -
752A ARG* 5.8 0.2 - - - -
753A ALA* 3.6 25.8 + - + +
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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