Contacts of the helix formed by residues 741 - 748 (chain M) in PDB entry 1MVW
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 741 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505M MLY 2.6 61.4 + - + +
506M GLU* 4.1 14.9 + - - -
717M TYR* 3.9 37.4 - - + -
739M ASP* 2.6 13.7 + - - +
740M SER* 1.3 77.1 - - - +
742M LYS* 1.3 60.0 + - + +
743M ALA 2.7 15.5 + - - -
744M SER* 3.0 15.9 + - - -
745M GLU* 3.2 18.8 + - + +
762M HIS 5.6 1.1 - - - +
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Residues in contact with LYS 742 (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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735M GLY* 3.7 0.9 - - - -
738M MET* 5.7 3.6 - - + +
739M ASP* 2.7 39.7 + - + +
741M LYS* 1.3 76.5 - - - +
743M ALA* 1.3 49.7 + - - +
745M GLU* 2.8 14.5 - - + +
746M LYS* 2.8 57.0 + - + +
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Residues in contact with ALA 743 (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 LYS* 3.9 2.0 - - + -
735M GLY* 1.9 37.2 + - - +
736M GLN* 2.0 41.1 - - + +
739M ASP 2.5 15.1 + - - +
740M SER 4.2 1.8 - - - +
741M LYS 2.7 0.6 + - - -
742M LYS* 1.3 66.9 - - - +
744M SER* 1.4 51.5 + - - +
745M GLU 2.8 3.6 - - - -
746M LYS* 2.6 9.5 + - - +
747M LEU* 2.6 33.2 + - - -
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Residues in contact with SER 744 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717M TYR* 2.9 53.9 + - - -
720M PHE* 3.3 26.5 - - - -
721M LYS 4.6 1.2 + - - -
736M GLN* 4.2 4.1 - - - +
740M SER 3.8 4.2 + - - -
741M LYS 3.0 4.1 + - - -
743M ALA* 1.4 72.7 - - - +
745M GLU* 1.3 66.8 + - - +
747M LEU* 3.6 4.8 - - - +
748M LEU* 3.1 30.1 + - - +
760M PHE* 4.5 1.1 - - - -
765M VAL* 4.9 1.1 - - - -
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Residues in contact with GLU 745 (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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506M GLU* 4.2 10.5 - - - +
741M LYS* 3.2 20.2 + - - +
742M LYS* 2.8 23.6 - - + +
743M ALA 2.8 0.2 + - - -
744M SER* 1.3 82.0 - - - +
746M LYS* 1.3 67.3 + - - +
748M LEU* 3.1 13.9 + - - +
749M GLY* 3.8 2.4 + - - -
760M PHE* 3.6 40.7 - - + -
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Residues in contact with LYS 746 (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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731M ALA* 4.4 13.5 - - + +
735M GLY* 3.9 15.0 - - - +
742M LYS* 3.5 31.6 - - + +
743M ALA 2.6 11.9 + - - +
745M GLU* 1.3 77.9 - - + +
747M LEU* 1.3 63.1 + - - +
749M GLY* 2.9 16.8 + - - -
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Residues in contact with LEU 747 (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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720M PHE* 4.8 8.7 - - + -
724M TYR* 3.7 7.0 - - + +
725M ARG* 3.6 4.7 - - - -
727M LEU* 4.5 5.4 - - + -
728M ASN* 4.6 0.6 - - + +
731M ALA* 4.3 2.5 + - - +
732M ILE* 0.6 137.5 - - + +
736M GLN* 3.6 6.1 - - - +
743M ALA 2.6 19.7 + - - +
744M SER* 3.6 12.6 - - - +
745M GLU 3.1 0.2 - - - -
746M LYS* 1.3 66.9 - - - +
748M LEU* 1.3 62.7 + - + +
749M GLY 2.5 16.8 + - - -
750M GLY* 3.0 14.7 + - - +
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Residues in contact with LEU 748 (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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720M PHE* 3.6 29.4 - - + -
744M SER* 3.1 25.8 + - - +
745M GLU 3.1 10.0 + - - +
747M LEU* 1.3 81.8 - - + +
749M GLY* 1.3 61.6 - - - +
750M GLY 3.0 9.6 - - - +
753M VAL* 5.1 8.9 - - + +
755M HIS* 3.0 22.2 + - - -
758M TYR* 3.5 46.9 - - + +
760M PHE* 4.5 12.3 - - + -
765M VAL* 5.2 2.9 - - + -
767M PHE* 4.3 17.0 - - + -
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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