Contacts of the helix formed by residues 686 - 695 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441M PHE* 4.8 4.6 - - - -
462M GLN* 4.4 2.5 - - - -
553M PHE* 4.2 20.2 - - - -
554M ALA* 4.9 2.5 - - - -
660M ARG* 4.3 6.7 - - - -
682M LEU 4.2 0.2 - - - -
683M ARG 3.3 11.0 + - - -
684M ALA 3.6 0.8 - - - -
685M CYS* 1.3 77.4 - - - +
687M VAL* 1.4 57.3 + - - +
688M LEU 3.5 2.0 - - - -
689M GLU* 3.6 6.4 + - - +
690M THR* 2.9 36.0 + - - -
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Residues in contact with VAL 687 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74M LEU* 5.0 1.3 - - + -
85M VAL* 5.0 4.0 - - + -
103M CYS* 4.4 11.7 - - + -
106M VAL* 5.6 2.2 - - + -
108M VAL* 4.9 13.2 - - + -
660M ARG* 4.3 15.3 - - + -
662M ILE* 5.2 0.9 - - + -
682M LEU* 3.3 31.6 + - + +
685M CYS* 3.9 29.6 - - + +
686M GLY* 1.4 78.4 - - - +
688M LEU* 1.3 61.1 + - + +
690M THR* 3.4 5.3 + - - -
691M ILE* 3.0 52.1 + - + +
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Residues in contact with LEU 688 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M HIS 5.3 0.2 - - - -
82M GLU* 3.5 47.3 - - + +
85M VAL* 4.0 39.7 - - + -
679M VAL* 4.6 4.9 - - + -
682M LEU* 3.9 32.3 + - + +
683M ARG* 4.1 22.4 - - + +
687M VAL* 1.3 75.7 - - + +
689M GLU* 1.3 57.1 + - - +
691M ILE* 3.5 9.4 - - + +
692M ARG* 2.9 27.6 + - - +
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Residues in contact with GLU 689 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551M LYS* 4.9 3.0 + - - -
553M PHE* 3.4 57.6 - - + +
554M ALA* 4.4 16.0 - - + +
683M ARG* 6.2 0.4 - - - +
686M GLY* 3.6 5.2 + - - +
687M VAL 3.4 0.4 - - - -
688M LEU* 1.3 75.0 - - - +
690M THR* 1.4 62.6 + - - +
692M ARG* 2.6 55.8 + - - +
693M ILE* 3.0 27.3 + - + +
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Residues in contact with THR 690 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M CYS* 5.1 12.6 - - - +
106M VAL* 5.5 2.9 - - + -
462M GLN* 3.6 19.8 + - - -
465M PHE* 3.7 27.8 - - + -
469M VAL* 5.7 3.6 - - + -
553M PHE* 4.3 3.2 - - - -
660M ARG* 5.2 1.7 + - - -
686M GLY 2.9 28.0 + - - -
687M VAL* 3.6 5.8 - - - -
689M GLU* 1.4 70.9 - - - +
691M ILE* 1.3 58.5 + - - +
693M ILE* 3.2 11.3 + - + +
694M SER* 3.0 34.2 + - - +
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Residues in contact with ILE 691 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74M LEU* 4.2 4.7 - - + -
75M THR* 6.5 0.2 - - + -
80M LEU* 3.4 41.8 - - + +
81M HIS* 4.8 2.7 - - - +
85M VAL* 3.6 32.5 - - + -
103M CYS* 3.4 29.8 - - - -
687M VAL* 3.0 32.7 + - + +
688M LEU* 3.5 9.4 - - + +
690M THR* 1.3 73.5 - - - +
692M ARG* 1.4 63.9 + - - +
694M SER* 3.2 9.4 + - - +
695M ALA* 3.1 23.7 + - - +
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Residues in contact with ARG 692 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M LEU 5.8 1.3 - - - -
490M TYR* 3.9 26.3 + - - -
553M PHE* 6.1 0.2 - - - -
688M LEU 2.9 15.5 + - - +
689M GLU* 2.6 49.1 + - - +
691M ILE* 1.4 75.0 - - - +
693M ILE* 1.3 90.3 + - - +
695M ALA* 3.8 10.6 + - - +
696M ALA* 4.0 7.8 + - - +
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Residues in contact with ILE 693 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466M ASN* 6.5 0.2 - - - -
488M ASP 5.2 5.4 - - - +
490M TYR* 3.6 46.0 - - + +
553M PHE* 4.9 11.4 - - + -
689M GLU* 3.0 17.1 + - + +
690M THR* 3.2 9.8 + - + +
692M ARG* 1.3 109.5 - - - +
694M SER* 1.4 63.9 + - - +
696M ALA* 3.1 23.1 + - - +
697M GLY 4.2 1.2 + - - -
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Residues in contact with SER 694 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75M THR* 4.1 23.8 - - - +
80M LEU* 4.5 1.8 - - - -
103M CYS* 6.0 0.9 - - - -
469M VAL* 6.2 0.3 - - - +
690M THR* 3.0 21.8 + - - +
691M ILE* 3.2 12.5 + - - +
693M ILE* 1.4 75.4 - - - +
695M ALA* 1.3 61.1 + - - +
696M ALA 3.4 0.7 + - - -
697M GLY* 3.5 9.9 + - - -
698M PHE 4.6 0.2 + - - -
699M PRO* 3.7 17.9 - - - +
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Residues in contact with ALA 695 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M LEU* 4.2 28.9 - - + +
691M ILE 3.1 15.1 + - - +
692M ARG* 4.1 7.4 - - - +
693M ILE 3.2 0.6 + - - -
694M SER* 1.3 73.0 - - - +
696M ALA* 1.4 62.3 + - - +
697M GLY 3.4 5.1 + - - +
699M PRO* 4.2 9.4 - - - -
753M ALA* 3.6 25.7 + - + +
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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