Contacts of the helix formed by residues 986 - 994 (chain B) in PDB entry 1M8X
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 LEU 986 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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954B VAL* 5.2 3.4 - - + -
977B CYS* 4.0 23.3 - - + +
978B ILE* 3.6 33.4 - - + +
981B VAL* 4.2 16.6 - - + +
982B GLN 3.9 8.7 - - - +
983B PRO* 3.6 24.9 - - + +
984B GLN 3.2 1.8 - - - -
985B SER* 1.3 78.2 - - - +
987B GLN* 1.3 57.9 + - - +
988B PHE* 3.1 9.9 - - + -
989B ILE* 2.8 46.6 + - + +
990B ILE* 3.1 19.7 - - + +
1013B ILE* 5.8 0.2 - - + -
1016B HIS* 5.9 0.4 - - + -
1017B CYS* 4.8 9.9 - - - -
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Residues in contact with GLN 987 (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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984B GLN 3.4 15.7 + - - +
985B SER 3.2 2.0 - - - -
986B LEU* 1.3 77.9 - - - +
988B PHE* 1.3 57.6 + - - +
989B ILE 3.2 0.2 - - - -
990B ILE* 3.4 18.0 + - - +
991B ASP* 2.5 52.1 + - - +
1020B ASP* 4.1 9.6 + - - +
1021B GLN* 3.2 33.1 + - - +
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Residues in contact with PHE 988 (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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954B VAL* 3.6 35.2 - - + -
955B ARG* 5.3 2.0 - - - -
957B LEU* 3.8 9.2 - - + -
958B ASP* 3.3 52.3 - - + +
961B VAL* 3.6 20.6 - - + -
985B SER 3.3 24.5 - - - -
986B LEU* 3.1 4.3 - - + -
987B GLN* 1.3 76.3 - - - +
989B ILE* 1.3 82.9 + - + +
991B ASP* 4.0 8.3 - - - +
992B ALA* 3.0 30.1 + - - +
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Residues in contact with ILE 989 (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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954B VAL* 6.5 0.2 - - + -
961B VAL* 4.0 18.4 - - + -
974B VAL* 4.0 24.7 - - + +
977B CYS* 4.8 5.6 - - + -
978B ILE* 4.4 8.1 - - + -
986B LEU* 2.8 37.7 + - + +
988B PHE* 1.3 98.1 - - + +
990B ILE* 1.3 64.9 + - + +
992B ALA* 3.3 2.3 + - - +
993B PHE* 3.1 47.1 + - + -
1013B ILE* 4.0 19.1 - - + -
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Residues in contact with ILE 990 (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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986B LEU* 3.1 22.7 - - + +
987B GLN* 3.4 22.0 + - - +
988B PHE 3.3 0.4 - - - -
989B ILE* 1.3 77.7 - - + +
991B ASP* 1.3 60.5 - - - +
993B PHE* 2.6 36.1 + - - +
994B LYS* 3.4 3.8 + - - -
1013B ILE* 4.4 12.3 - - + -
1017B CYS* 3.7 27.4 - - - -
1021B GLN* 3.8 39.5 - - + +
1024B PRO* 4.0 15.3 - - + -
1025B ILE* 4.5 8.9 - - + +
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Residues in contact with ASP 991 (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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987B GLN* 2.5 46.8 + - - +
988B PHE* 4.1 7.8 - - - +
990B ILE* 1.3 78.2 - - - +
992B ALA* 1.3 58.5 + - - +
993B PHE 3.5 0.5 + - - -
994B LYS* 3.5 21.4 - - - +
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Residues in contact with ALA 992 (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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961B VAL* 3.6 30.3 - - + -
962B LEU* 3.2 24.9 - - + +
988B PHE 3.0 20.3 + - - +
989B ILE 3.5 6.3 - - - +
990B ILE 3.0 0.8 - - - -
991B ASP* 1.3 75.7 - - - +
993B PHE* 1.3 62.3 + - - +
994B LYS* 3.3 1.9 + - - +
996B GLN* 4.2 6.4 - - - +
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Residues in contact with PHE 993 (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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961B VAL* 4.1 8.5 - - + -
962B LEU* 5.0 5.2 - - + -
965B VAL* 3.7 24.0 - - + -
989B ILE* 3.1 28.5 + - + -
990B ILE* 2.6 19.7 + - - +
992B ALA* 1.3 75.8 - - - +
994B LYS* 1.3 65.8 + - - +
995B GLY 3.3 0.3 + - - -
996B GLN* 2.7 21.0 + - - +
997B VAL* 3.3 12.1 + - + +
1000B LEU* 3.4 31.9 - - + -
1009B VAL* 3.3 35.2 - - + -
1010B ILE* 4.6 12.1 - - + -
1013B ILE* 4.2 12.6 - - + -
1025B ILE* 4.0 24.9 - - + -
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Residues in contact with LYS 994 (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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990B ILE 3.4 5.8 + - - +
991B ASP* 3.5 18.6 - - - +
992B ALA 3.3 1.9 - - - +
993B PHE* 1.3 76.1 - - - +
995B GLY* 1.3 61.5 + - - +
996B GLN* 2.9 18.7 + - - +
997B VAL* 5.5 0.2 - - - -
1024B PRO* 5.6 11.7 - - + -
1028B GLU* 4.4 7.2 - - - +
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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