Contacts of the helix formed by residues 723 - 733 (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 ASP 723 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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721M LEU* 3.4 10.8 - - + +
722M SER* 1.4 76.6 - - - +
724M ARG* 1.3 61.8 + - - +
725M LYS* 2.9 17.3 + - - +
726M GLN* 2.7 36.5 + - + +
727M THR* 2.7 31.0 + - - -
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Residues in contact with ARG 724 (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* 5.3 3.4 - - + +
705M GLN* 2.7 41.5 + - - +
708M PHE* 3.2 63.4 - - + +
709M SER* 4.6 2.4 + - - -
721M LEU 4.8 2.9 - - - +
722M SER 3.5 8.9 + - - +
723M ASP* 1.3 76.7 + - - +
725M LYS* 1.4 63.5 + - - +
727M THR* 3.6 6.4 - - - -
728M CYS* 3.2 28.6 + - - -
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Residues in contact with LYS 725 (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* 3.5 49.4 - - + +
723M ASP* 2.9 13.3 + - - +
724M ARG* 1.4 76.8 - - - +
726M GLN* 1.3 63.9 + - - +
728M CYS* 3.2 8.0 + - - +
729M LYS* 3.2 23.5 + - + +
744M PHE* 5.6 3.4 - - - -
745M GLY 2.6 27.0 + - - -
746M LYS* 2.8 21.4 + - - +
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Residues in contact with GLN 726 (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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721M LEU* 4.2 11.4 - - + -
723M ASP* 2.7 30.9 + - + +
725M LYS* 1.3 73.7 - - - +
727M THR* 1.3 61.4 + - - +
729M LYS* 3.2 35.0 + - - +
730M ASN* 2.9 59.1 + - - +
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Residues in contact with THR 727 (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* 4.1 9.7 - - + -
715M MET* 3.7 29.2 - - + -
719M ASP 3.7 17.5 - - - +
720M VAL* 4.0 5.8 - - - -
721M LEU* 2.9 21.8 + - - +
723M ASP 2.7 22.9 + - - -
724M ARG* 3.6 10.2 - - - -
725M LYS 3.3 0.4 - - - -
726M GLN* 1.3 77.0 - - - +
728M CYS* 1.3 61.7 + - - +
730M ASN* 3.3 12.4 + - - +
731M VAL* 3.1 24.3 + - + +
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Residues in contact with CYS 728 (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* 3.5 43.1 - - + -
707M PHE* 3.7 30.2 - - + -
708M PHE* 3.9 15.5 - - - -
715M MET* 5.2 2.0 - - - -
724M ARG 3.2 16.6 + - - -
725M LYS 3.2 8.1 + - - +
727M THR* 1.3 74.5 - - - +
729M LYS* 1.4 66.0 + - - +
731M VAL* 4.2 2.4 - - - +
732M LEU* 3.2 28.9 + - - +
744M PHE* 4.7 1.8 - - - -
749M ILE* 4.6 2.2 - - + -
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Residues in contact with LYS 729 (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* 5.4 1.3 - - + -
725M LYS* 3.2 14.3 + - - +
726M GLN* 3.2 37.2 + - - +
728M CYS* 1.4 79.2 - - - +
730M ASN* 1.3 62.4 + - - +
732M LEU* 4.2 0.3 - - - -
733M GLU* 2.6 68.8 + - - +
744M PHE* 3.4 40.8 - - + -
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Residues in contact with ASN 730 (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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719M ASP* 4.7 7.5 + - + +
721M LEU* 3.5 29.1 - - - +
726M GLN* 2.9 39.0 + - - +
727M THR* 3.6 7.2 - - - +
729M LYS* 1.3 76.6 - - - +
731M VAL* 1.3 63.3 + - + +
733M GLU* 3.8 13.4 + - - +
734M LYS* 3.0 35.8 - - - +
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Residues in contact with VAL 731 (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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707M PHE* 5.1 6.7 - - + -
711M TYR* 5.5 1.8 - - + +
714M LEU* 5.2 3.8 - - + -
715M MET* 3.8 51.1 - - + +
719M ASP* 4.7 15.0 - - + +
727M THR* 3.1 21.3 + - + +
728M CYS* 4.2 4.7 - - - +
730M ASN* 1.3 73.5 - - + +
732M LEU* 1.3 65.8 + - - +
734M LYS* 3.2 18.0 + - - +
735M LEU* 3.2 30.4 + - + +
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Residues in contact with LEU 732 (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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707M PHE* 3.9 15.7 - - + -
728M CYS 3.2 17.1 + - - +
729M LYS 4.2 2.2 - - - +
731M VAL* 1.3 78.3 - - - +
733M GLU* 1.3 56.6 + - - +
734M LYS 3.1 1.0 + - - -
735M LEU* 3.1 6.4 + - + -
736M ILE* 2.9 49.5 + - + +
742M TYR* 3.4 34.3 - - + -
744M PHE* 3.9 13.0 - - + -
749M ILE* 4.0 5.6 - - + -
751M PHE* 3.5 26.9 - - + -
759M LEU* 3.8 28.9 - - + -
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Residues in contact with GLU 733 (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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729M LYS* 2.6 55.9 + - - +
730M ASN* 4.1 7.9 + - - +
731M VAL 3.3 1.0 - - - -
732M LEU* 1.3 72.2 - - - +
734M LYS* 1.3 64.3 + - - +
736M ILE 4.0 5.8 - - - -
737M LEU* 5.2 5.0 - - - +
739M LYS* 2.6 31.9 + - + +
742M TYR* 3.3 22.9 - - + +
744M PHE* 3.4 4.7 - - + -
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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