Contacts of the helix formed by residues 1054 - 1066 (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 ARG1054 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023B LEU* 4.1 26.0 - - - +
1026B LEU* 4.5 12.7 - - + +
1027B GLU* 5.4 2.6 - - - +
1053B GLY* 1.3 73.1 - - - -
1055B PRO* 1.3 64.5 - - + +
1056B GLU* 2.9 37.2 + - - +
1057B ASP* 2.7 71.2 + - - +
1058B LYS* 3.0 12.2 + - - +
1060B LYS* 4.9 7.1 - - - +
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Residues in contact with PRO1055 (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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1053B GLY 4.0 4.9 - - - +
1054B ARG* 1.3 85.1 - - + +
1056B GLU* 1.3 70.9 + - - +
1058B LYS* 3.1 23.3 + - + +
1059B SER* 2.9 34.5 + - - -
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Residues in contact with GLU1056 (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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1054B ARG* 2.9 38.4 + - + +
1055B PRO* 1.3 94.7 - - - +
1057B ASP* 1.3 58.6 + - - +
1059B SER* 3.9 7.3 + - - -
1060B LYS* 3.1 35.4 + - - +
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Residues in contact with ASP1057 (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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1026B LEU* 3.4 21.2 - - - +
1030B HIS* 2.6 50.1 + - + +
1049B VAL* 3.9 15.5 - - + -
1054B ARG* 2.7 67.5 + - - +
1056B GLU* 1.3 69.8 - - - +
1058B LYS* 1.3 63.7 + - - +
1060B LYS* 3.1 12.0 + - - -
1061B ILE* 3.2 7.1 + - - +
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Residues in contact with LYS1058 (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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1049B VAL* 3.8 16.2 - - - +
1050B LEU* 3.5 38.2 + - + +
1052B HIS 6.0 0.2 - - - -
1053B GLY 4.6 5.2 - - - +
1054B ARG 3.0 17.9 + - - +
1055B PRO* 3.5 20.6 - - + +
1057B ASP* 1.3 75.8 - - - +
1059B SER* 1.3 51.2 + - - +
1061B ILE* 2.7 28.8 + - - +
1062B VAL* 2.8 22.4 + - + +
1088B HIS* 2.7 39.1 + - + +
1089B ALA* 5.3 0.7 - - - +
1090B SER 6.0 0.4 - - - +
1093B GLU* 5.9 1.1 - - - +
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Residues in contact with SER1059 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055B PRO* 2.9 19.7 + - - +
1056B GLU* 4.0 7.8 - - - -
1058B LYS* 1.3 75.3 - - - +
1060B LYS* 1.3 57.5 + - - +
1062B VAL* 3.8 5.2 - - - +
1063B ALA* 2.9 29.6 + - - +
1090B SER* 5.6 1.0 - - - -
1093B GLU* 2.7 31.1 + - - +
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Residues in contact with LYS1060 (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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1027B GLU* 5.5 6.5 - - - +
1030B HIS* 3.4 50.4 + - + +
1033B THR* 5.2 1.3 - - - +
1054B ARG* 4.9 6.4 - - - +
1056B GLU* 3.1 25.6 - - - +
1057B ASP* 3.1 9.9 + - - +
1058B LYS 3.1 1.0 - - - -
1059B SER* 1.3 77.3 - - - +
1061B ILE* 1.3 62.0 + - - +
1063B ALA* 3.6 7.0 + - - +
1064B GLU* 3.3 26.0 + - - +
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Residues in contact with ILE1061 (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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1030B HIS* 4.4 8.3 - - + +
1033B THR* 4.3 22.0 - - + +
1046B ILE* 3.6 52.3 - - + +
1049B VAL* 4.0 21.1 - - + -
1050B LEU* 3.8 21.5 - - + -
1057B ASP 3.7 10.8 - - - +
1058B LYS* 2.7 13.6 + - - +
1060B LYS* 1.3 70.0 - - - +
1062B VAL* 1.3 65.2 + - - +
1064B GLU* 3.2 13.9 + - - +
1065B ILE* 3.2 14.6 + - + +
1081B VAL* 4.4 4.3 - - + -
1085B CYS* 3.9 11.2 - - - -
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Residues in contact with VAL1062 (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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1050B LEU* 4.6 4.7 - - + -
1058B LYS* 2.8 24.2 + - + +
1059B SER* 3.8 4.7 - - - +
1061B ILE* 1.3 73.5 - - - +
1063B ALA* 1.3 62.9 + - - +
1065B ILE* 2.9 3.8 + - - +
1066B ARG* 2.8 30.0 + - + +
1085B CYS* 3.9 26.7 - - + -
1088B HIS 5.9 0.2 - - - -
1089B ALA* 4.1 14.1 - - + -
1093B GLU* 3.9 36.3 - - + +
1097B LEU* 3.9 24.0 - - + -
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Residues in contact with ALA1063 (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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1059B SER 2.9 19.1 + - - +
1060B LYS* 3.7 9.0 - - - +
1061B ILE 3.3 0.2 - - - -
1062B VAL* 1.3 75.9 - - - +
1064B GLU* 1.3 68.3 + - - +
1066B ARG* 3.2 29.9 - - - +
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Residues in contact with GLU1064 (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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1030B HIS 5.1 3.6 - - - +
1033B THR* 3.6 34.3 + - + -
1034B GLU* 4.4 16.4 + - + +
1060B LYS 3.3 16.4 - - - +
1061B ILE 3.2 7.8 + - - +
1062B VAL 3.1 0.4 - - - -
1063B ALA* 1.3 80.6 - - - +
1065B ILE* 1.3 56.3 + - + +
1066B ARG 3.7 0.3 - - - +
1068B ASN* 2.8 31.7 + - - -
1072B LEU* 4.8 1.2 - - - +
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Residues in contact with ILE1065 (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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1037B VAL* 4.4 15.7 - - + -
1061B ILE* 3.4 14.6 - - + +
1062B VAL 2.9 7.9 + - - +
1064B GLU* 1.3 80.1 - - + +
1066B ARG* 1.3 68.1 + - - +
1067B GLY 3.1 0.2 + - - -
1068B ASN* 2.8 19.2 + - - -
1069B VAL* 3.3 16.1 + - + -
1072B LEU* 4.1 22.7 - - + -
1081B VAL* 4.3 14.8 - - + -
1082B VAL* 4.5 20.4 - - + -
1085B CYS* 3.6 30.3 - - + -
1097B LEU* 3.8 21.5 - - + -
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Residues in contact with ARG1066 (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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1062B VAL* 2.8 24.1 + - + +
1063B ALA* 3.2 23.2 - - - +
1064B GLU 3.7 0.3 - - - +
1065B ILE* 1.3 77.0 - - - +
1067B GLY* 1.3 58.3 + - - +
1068B ASN* 3.4 9.4 + - - -
1093B GLU* 5.2 5.0 - - - +
1096B VAL* 3.0 39.4 - - - +
1097B LEU* 3.6 20.9 - - + -
1100B GLU* 3.7 9.7 + - - +
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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