Contacts of the helix formed by residues 912 - 925 (chain B) in PDB entry 1M2V
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 SER 912 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715B HIS* 3.8 2.8 + - - -
904B GLU 3.7 7.4 - - - -
905B ASP* 3.4 9.9 - - - -
906B LYS* 3.7 22.3 - - - +
911B GLU* 1.3 78.1 + - - +
913B TYR* 1.3 64.9 + - - +
914B ARG* 4.0 7.9 + - - +
915B GLU* 3.3 21.6 + - - +
916B PHE* 2.9 21.0 + - - +
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Residues in contact with TYR 913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 4.1 16.6 + - - +
146B GLU 5.7 0.7 - - - -
147B LEU* 5.5 6.3 - - + -
149B PRO* 3.4 36.6 - - + +
708B ARG 4.6 2.9 + - - -
711B PRO* 4.2 0.7 - - - +
712B LEU* 3.6 49.1 + - + +
715B HIS* 3.8 15.8 + + + -
904B GLU* 2.8 35.0 + - + +
912B SER* 1.3 71.3 - - - +
914B ARG* 1.3 66.2 + - + +
916B PHE* 3.0 33.0 + + - +
917B LEU* 3.2 47.2 + - + +
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Residues in contact with ARG 914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 6.0 0.2 - - - -
147B LEU* 2.8 52.5 - - + +
148B PRO* 3.5 23.2 - - - +
904B GLU 4.8 0.2 + - - -
912B SER* 3.3 7.0 + - - +
913B TYR* 1.3 79.4 - - + +
915B GLU* 1.3 61.2 + - - +
917B LEU* 3.4 10.9 + - - +
918B GLN* 2.9 34.7 + - + +
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Residues in contact with GLU 915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911B GLU* 3.0 32.3 - - - +
912B SER* 3.3 21.7 + - - +
913B TYR 3.2 0.6 - - - -
914B ARG* 1.3 76.8 - - - +
916B PHE* 1.3 56.4 + - - +
918B GLN* 3.1 18.8 + - - +
919B ILE* 2.6 51.5 + - + +
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Residues in contact with PHE 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676B ASN* 3.8 24.2 - - - -
679B VAL* 3.8 32.8 - - + -
711B PRO* 3.4 24.7 - - + -
714B MET 5.4 0.4 - - - -
715B HIS* 3.4 41.3 - + + +
911B GLU* 4.6 2.4 - - + +
912B SER 2.9 13.9 + - - +
913B TYR* 3.0 25.1 - + - +
915B GLU* 1.3 75.7 - - - +
917B LEU* 1.3 55.3 + - + +
919B ILE* 2.9 19.3 + - + +
920B MET* 2.8 51.1 + - + +
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Residues in contact with LEU 917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 3.7 35.7 - - + +
144B LEU* 3.8 17.3 - - + -
147B LEU* 4.5 10.1 - - + -
683B LEU* 5.3 1.8 - - + -
701B LEU* 3.6 27.9 - - + +
711B PRO* 4.5 7.6 - - + -
913B TYR* 3.2 53.8 + - + +
914B ARG* 3.7 6.7 - - - +
916B PHE* 1.3 82.5 - - + +
918B GLN* 1.3 58.0 + - - +
920B MET* 4.3 4.0 - - + -
921B LYS* 2.8 33.7 + - - +
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Residues in contact with GLN 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 2.9 38.4 - - - +
914B ARG* 2.9 30.7 + - + +
915B GLU* 3.1 25.1 + - - +
917B LEU* 1.3 75.1 - - - +
919B ILE* 1.3 62.1 + - - +
921B LYS* 3.8 9.6 + - - +
922B ALA* 3.3 21.7 + - - +
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Residues in contact with ILE 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911B GLU* 3.5 33.9 - - + -
915B GLU* 2.6 42.1 + - + +
916B PHE* 2.9 13.8 + - + +
918B GLN* 1.3 70.7 - - - +
920B MET* 1.3 66.1 + - + +
922B ALA* 3.1 8.2 + - - +
923B ARG* 2.8 51.1 + - + +
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Residues in contact with MET 920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676B ASN* 4.5 5.2 - - - +
679B VAL* 4.1 20.6 - - + +
680B GLN* 3.2 52.7 - - + +
683B LEU* 4.1 16.2 - - + -
916B PHE* 2.8 46.8 + - + +
917B LEU* 3.8 7.0 - - + +
919B ILE* 1.3 70.6 - - + +
921B LYS* 1.3 68.2 + - - +
923B ARG* 3.0 21.9 + - - +
924B ILE* 2.9 32.0 + - + +
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Residues in contact with LYS 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 3.7 20.9 - - + +
699B ALA* 2.7 50.8 + - - +
700B PRO 4.1 8.1 - - - +
701B LEU* 3.9 23.1 - - + +
917B LEU 2.8 22.1 + - - +
918B GLN* 3.8 11.7 + - - +
920B MET* 1.3 73.5 - - - +
922B ALA* 1.3 64.8 + - - +
924B ILE* 3.2 4.9 + - + +
925B SER* 2.8 39.5 + - - +
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Residues in contact with ALA 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918B GLN 3.3 10.6 + - - +
919B ILE* 3.1 11.1 + - - +
921B LYS* 1.3 80.5 - - - +
923B ARG* 1.3 65.4 + - + +
925B SER* 3.2 22.8 + - - +
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Residues in contact with ARG 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676B ASN* 4.9 15.2 - - - +
680B GLN* 3.0 34.9 + - - +
919B ILE* 2.8 46.9 + - + +
920B MET* 3.0 24.1 + - + +
922B ALA* 1.3 79.0 - - + +
924B ILE* 1.3 61.4 + - - +
925B SER 3.6 5.0 - - - +
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Residues in contact with ILE 924 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680B GLN* 3.9 26.7 - - + +
683B LEU* 3.9 20.9 - - + +
684B ALA* 3.9 18.2 - - + +
687B LYS* 3.0 34.7 + - + +
701B LEU* 3.9 26.7 - - + -
702B ARG 6.2 0.2 - - - +
920B MET* 2.9 28.3 + - + +
921B LYS* 3.2 10.8 - - + +
923B ARG* 1.3 71.9 - - - +
925B SER* 1.3 70.9 + - - +
926B LYS* 3.5 3.3 + - - +
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Residues in contact with SER 925 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687B LYS* 3.1 14.2 + - - +
921B LYS* 2.8 37.7 + - - +
922B ALA* 3.2 19.2 + - - +
923B ARG 3.6 4.5 - - - +
924B ILE* 1.3 82.5 - - - +
926B LYS* 1.3 66.7 + - - +
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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