Contacts of the strand formed by residues 748 - 751 (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 LYS 748 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476M GLU* 2.6 43.8 + - - -
479M LYS* 6.1 0.2 - - - -
480M GLU* 2.9 28.5 + - - +
701M ARG* 4.2 17.0 - - + +
702M TRP 3.4 13.5 - - - +
703M THR* 4.5 11.2 - - + -
704M TYR* 2.8 27.2 + - - -
745M GLY* 3.0 16.6 + - - -
747M THR* 1.3 86.5 - - - +
749M ILE* 1.4 59.4 + - - +
750M PHE* 3.9 13.0 - - + -
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Residues in contact with ILE 749 (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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700M SER 3.7 1.0 - - - +
701M ARG* 3.4 7.1 - - - +
702M TRP 2.9 32.0 + - - +
703M THR 4.8 0.4 - - - +
704M TYR* 3.5 31.6 - - + -
707M PHE* 3.7 46.2 - - + -
728M CYS* 4.6 1.6 - - + -
732M LEU* 4.0 6.7 - - + -
742M TYR* 4.5 3.1 - - + -
743M GLN 3.6 11.0 - - - +
744M PHE* 3.7 24.2 - - + -
748M LYS* 1.4 71.3 - - - +
750M PHE* 1.3 67.1 + - - +
751M PHE* 3.6 26.2 - - + -
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Residues in contact with PHE 750 (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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476M GLU* 3.3 27.4 - - + -
477M TYR* 4.0 20.4 - + - -
480M GLU* 3.7 21.1 - - + -
482M ILE* 3.4 34.1 - - + -
698M PHE* 3.4 24.9 - + + -
700M SER 3.7 4.0 - - - -
701M ARG* 3.5 37.0 - - + -
742M TYR* 3.2 6.9 - - - +
743M GLN* 2.9 40.1 + - + +
748M LYS* 3.9 17.7 - - + -
749M ILE* 1.3 78.7 - - - +
751M PHE* 1.3 59.7 + - - +
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Residues in contact with PHE 751 (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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698M PHE* 3.4 14.0 - - - +
699M PRO 3.4 0.2 - - - -
700M SER* 2.8 48.1 + - - +
702M TRP* 4.3 18.2 - + + -
707M PHE* 3.6 27.8 - + - -
732M LEU* 3.5 29.2 - - + -
736M ILE* 4.7 2.0 - - + -
741M LYS 3.9 1.8 - - - -
742M TYR* 4.0 10.5 - + + -
749M ILE* 3.6 36.1 - - + -
750M PHE* 1.3 72.4 - - - +
752M ARG* 1.4 67.5 + - - +
755M GLN* 4.2 16.2 - - + -
756M VAL* 4.1 15.3 - - + -
759M LEU* 4.1 13.5 - - + -
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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