Contacts of the helix formed by residues 704 - 712 (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 TYR 704 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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703M THR* 1.3 74.2 - - - +
705M GLN* 1.4 56.2 + - - +
707M PHE* 3.7 2.2 + - - -
708M PHE* 3.1 30.7 + - - +
724M ARG* 5.0 3.0 - - - +
725M LYS* 3.5 61.5 - - + +
728M CYS* 3.5 22.8 - - + -
729M LYS* 5.9 1.3 - - + -
744M PHE* 3.5 24.1 - + - +
745M GLY 3.0 18.8 + - - -
746M LYS 4.5 0.2 - - - -
747M THR* 3.3 32.3 - - - -
748M LYS 2.8 22.7 + - - -
749M ILE* 3.5 18.2 - - + -
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Residues in contact with GLN 705 (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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703M THR* 3.1 9.7 + - - +
704M TYR* 1.4 75.7 - - - +
706M GLU* 1.4 75.0 + - + +
708M PHE* 3.5 2.3 + - - +
709M SER* 3.1 41.2 + - - -
724M ARG* 2.7 47.7 + - - +
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Residues in contact with GLU 706 (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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701M ARG 5.3 0.2 - - - +
702M TRP* 3.7 28.1 - - + -
703M THR* 2.6 60.6 + - - +
705M GLN* 1.4 82.4 - - + +
707M PHE* 1.4 65.8 + - - +
709M SER* 3.3 16.0 + - - -
710M ARG* 3.3 11.1 + - - +
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Residues in contact with PHE 707 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702M TRP* 3.6 15.1 - + + -
703M THR 3.1 17.4 + - - +
704M TYR 4.0 2.9 - - - +
706M GLU* 1.4 75.2 - - - +
708M PHE* 1.3 63.8 + - - +
711M TYR* 3.1 55.5 + + + +
715M MET* 5.1 2.9 - - + -
728M CYS* 3.7 38.8 - - + -
731M VAL* 5.1 6.7 - - + -
732M LEU* 3.9 28.0 - - + -
735M LEU* 5.1 5.6 - - + -
749M ILE* 3.7 13.9 - - + -
751M PHE* 3.6 34.1 - + - -
759M LEU* 3.7 19.5 - - + -
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Residues in contact with PHE 708 (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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704M TYR 3.1 20.1 + - - +
705M GLN 3.6 4.3 - - - +
707M PHE* 1.3 77.9 - - - +
709M SER* 1.3 59.5 + - - +
712M ARG* 2.9 58.7 + - + +
715M MET* 4.3 14.8 - - + -
720M VAL* 4.4 13.9 - - + -
721M LEU 5.4 0.4 - - - -
724M ARG* 3.2 73.1 - - + +
727M THR* 4.1 17.3 - - + -
728M CYS* 3.9 9.4 - - - -
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Residues in contact with SER 709 (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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705M GLN* 3.1 32.1 + - - -
706M GLU* 3.3 10.5 + - - -
708M PHE* 1.3 81.5 - - - +
710M ARG* 1.3 62.3 + - - +
712M ARG* 4.0 9.3 + - - +
724M ARG* 4.6 2.8 + - - -
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Residues in contact with ARG 710 (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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67M ILE* 3.3 47.9 - - - +
702M TRP* 4.0 15.5 - - + -
706M GLU 3.3 12.0 + - - +
709M SER* 1.3 79.2 - - - +
711M TYR* 1.4 71.5 + - + +
712M ARG 3.6 0.6 + - - -
713M VAL* 4.0 10.2 - - - +
760M GLU* 2.7 43.3 + - - +
763M ARG* 3.1 43.1 + - - +
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Residues in contact with TYR 711 (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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702M TRP* 3.8 32.2 - + - -
707M PHE* 3.1 52.6 + + + +
708M PHE 3.8 1.6 - - - -
710M ARG* 1.4 83.4 - - + +
712M ARG* 1.4 56.9 + - - +
713M VAL* 3.1 4.3 - - - -
714M LEU* 3.0 44.7 + - + +
715M MET* 3.5 13.8 - - + +
731M VAL* 5.5 1.5 - - + +
735M LEU* 5.8 2.7 - - + -
756M VAL* 4.2 1.4 - - - +
759M LEU* 3.7 42.8 - - + +
760M GLU* 2.7 38.5 + - - +
763M ARG* 3.6 15.3 - - + -
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Residues in contact with ARG 712 (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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708M PHE* 2.9 41.8 + - + +
709M SER* 4.2 8.3 - - - +
710M ARG 3.6 2.0 - - - -
711M TYR* 1.4 74.9 - - - +
713M VAL* 1.3 56.2 + - + +
714M LEU 3.3 3.0 + - - -
715M MET* 3.6 35.4 + - - +
717M GLN* 2.9 39.2 + - - +
720M VAL* 3.6 25.9 - - - +
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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