Contacts of the helix formed by residues 770 - 786 (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 GLY 770 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95M THR* 3.1 8.5 + - - -
96M HIS* 3.9 21.8 + - - -
769M ALA* 1.5 59.7 - - - +
771M LEU* 1.3 58.3 + - - +
773M GLY* 3.7 3.5 - - - -
774M LEU* 3.2 26.4 + - - +
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Residues in contact with LEU 771 (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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757M GLN* 3.8 0.4 - - - -
768M MLY 4.6 22.4 - - + -
769M ALA* 3.3 2.7 - - + +
770M GLY* 1.3 77.1 - - - +
772M LEU* 1.3 61.5 + - + +
773M GLY 2.8 3.8 - - - -
774M LEU* 2.3 40.1 + - + +
775M LEU* 2.7 34.9 + - + +
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Residues in contact with LEU 772 (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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757M GLN* 1.3 121.6 + - + +
768M MLY 1.5 104.5 - - + +
769M ALA 3.2 3.8 - - - +
771M LEU* 1.3 81.4 - - + +
773M GLY* 1.3 62.3 + - - +
775M LEU* 3.1 4.8 + - + +
776M GLU* 3.1 28.4 + - - +
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Residues in contact with GLY 773 (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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769M ALA 2.4 28.6 + - - -
770M GLY* 4.0 3.8 - - - -
771M LEU 2.8 0.8 - - - -
772M LEU* 1.3 71.8 - - - +
774M LEU* 1.3 64.0 + - - +
776M GLU* 3.6 6.7 - - - +
777M GLU* 3.4 18.4 + - - +
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Residues in contact with LEU 774 (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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35M MLY 5.6 10.5 - - - -
770M GLY 3.2 17.8 + - - +
771M LEU* 2.3 39.9 + - + +
773M GLY* 1.3 69.7 - - - +
775M LEU* 1.3 69.8 + - + +
777M GLU* 3.2 27.7 + - - +
778M MET* 3.3 37.9 + - + +
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Residues in contact with LEU 775 (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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754M ASP* 3.0 28.9 - - - +
756M THR* 5.4 0.9 - - + -
757M GLN* 3.4 29.8 - - - +
771M LEU* 2.7 31.1 + - + +
772M LEU* 3.1 8.0 + - + +
774M LEU* 1.3 77.9 - - + +
776M GLU* 1.3 64.0 + - - +
778M MET* 2.8 33.6 + - + +
779M ARG 3.0 7.8 + - - -
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Residues in contact with GLU 776 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752M ASP 3.4 2.3 - - - +
753M VAL* 1.7 57.9 - - + +
754M ASP* 1.2 73.7 + - + +
757M GLN* 4.9 3.1 - - + -
758M TYR* 6.0 0.2 - - - -
772M LEU 3.1 16.8 + - - +
773M GLY* 3.6 7.9 - - - +
775M LEU* 1.3 76.1 - - - +
777M GLU* 1.4 52.0 - - - +
779M ARG* 2.8 8.3 + - - +
780M ASP* 2.4 40.3 + - - +
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Residues in contact with GLU 777 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M MLY 4.8 12.7 - - - -
773M GLY 3.4 9.2 + - - +
774M LEU* 3.2 26.5 + - - +
775M LEU 3.0 1.0 + - - -
776M GLU* 1.4 77.7 - - - +
778M MET* 1.3 69.1 + - + +
780M ASP* 2.9 21.5 + - + +
781M ASP* 3.0 23.3 + - - +
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Residues in contact with MET 778 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774M LEU* 3.7 38.8 - - + +
775M LEU* 2.8 21.7 + - + +
777M GLU* 1.3 80.6 - - + +
779M ARG* 1.3 64.7 + - - +
781M ASP* 3.2 12.8 + - - +
782M MLY 3.0 25.2 + - + +
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Residues in contact with ARG 779 (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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751M GLY 2.0 27.1 + - - -
752M ASP* 1.7 76.8 - - - +
753M VAL* 1.9 64.3 + - - +
754M ASP* 3.1 11.0 - - - +
755M HIS* 2.5 29.1 + - - +
775M LEU 3.0 4.8 + - - +
776M GLU* 2.8 13.9 + - - +
778M MET* 1.3 80.3 - - - +
780M ASP* 1.3 47.3 + - - +
782M MLY 2.6 21.0 + - - -
783M LEU* 2.9 16.2 - - + +
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Residues in contact with ASP 780 (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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752M ASP* 1.7 61.7 + - - +
753M VAL* 4.6 4.5 - - - +
776M GLU* 2.4 24.8 + - - +
777M GLU* 2.9 14.2 + - + +
779M ARG* 1.3 67.1 - - - +
781M ASP* 1.3 66.8 + - - +
783M LEU 3.0 3.5 + - - -
784M ALA* 3.4 7.8 + - - +
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Residues in contact with ASP 781 (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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777M GLU* 3.0 19.6 + - - +
778M MET* 3.6 11.4 - - - +
780M ASP* 1.3 77.5 - - - +
782M MLY 1.3 67.3 + - + +
783M LEU 3.0 1.6 + - - -
784M ALA* 3.2 16.9 + - - +
785M GLU* 3.4 15.2 + - - +
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Residues in contact with MLY 782 (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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778M MET* 3.0 14.1 + - + +
779M ARG* 2.6 20.1 + - - +
781M ASP* 1.3 76.3 + - + +
783M LEU* 1.3 65.2 + - + +
785M GLU* 3.5 17.1 - - + +
786M ILE* 3.3 26.6 + - + +
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Residues in contact with LEU 783 (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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751M GLY 4.2 2.9 - - - +
752M ASP* 1.8 68.6 - - + +
779M ARG* 2.9 22.2 - - + +
780M ASP 3.0 2.8 + - - -
782M MLY 1.3 87.1 + - + +
784M ALA* 1.3 70.8 + - - +
785M GLU 3.0 1.3 - - - -
786M ILE* 3.0 39.7 + - + +
787M ILE* 3.8 7.1 - - - +
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Residues in contact with ALA 784 (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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752M ASP* 4.2 0.2 + - - -
780M ASP 3.4 8.3 + - - +
781M ASP* 3.2 12.5 + - - +
783M LEU* 1.3 77.0 - - - +
785M GLU* 1.3 65.5 - - - +
787M ILE* 3.4 8.2 - - - +
788M THR* 2.5 26.1 + - - +
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Residues in contact with GLU 785 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781M ASP 3.4 10.2 + - - +
782M MLY 3.5 22.9 - - + +
784M ALA* 1.3 77.7 - - - +
786M ILE* 1.3 51.3 + - + +
787M ILE 2.4 5.2 + - - -
788M THR* 2.1 52.5 + - - +
789M ALA* 3.8 2.6 + - - -
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Residues in contact with ILE 786 (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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782M MLY 3.3 16.1 + - + +
783M LEU* 3.0 32.0 + - + +
785M GLU* 1.3 74.1 - - + +
787M ILE* 1.2 119.9 + - + +
790M THR* 5.1 0.9 + - - -
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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