Contacts of the helix formed by residues 1090 - 1104 (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 SER1090 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1058B LYS* 6.0 0.4 - - - +
1059B SER* 5.6 0.7 - - - -
1089B ALA* 1.3 80.6 - - - +
1091B ARG* 1.3 65.1 + - - +
1092B THR* 3.7 6.6 + - - -
1093B GLU* 2.9 41.5 + - - +
1094B ARG* 3.0 20.3 + - - +
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Residues in contact with ARG1091 (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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1090B SER* 1.3 75.2 - - - +
1092B THR* 1.3 63.0 + - - +
1094B ARG* 3.5 22.9 + - - +
1095B ALA* 3.2 22.5 + - - +
1133B GLU* 3.3 38.5 + - - +
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Residues in contact with THR1092 (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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1090B SER* 3.3 6.6 + - - -
1091B ARG* 1.3 76.7 - - - +
1093B GLU* 1.3 64.0 + - + +
1095B ALA* 3.3 6.5 + - - +
1096B VAL* 2.9 39.5 + - + +
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Residues in contact with GLU1093 (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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1058B LYS* 5.9 0.5 - - - +
1059B SER* 2.7 35.5 + - - +
1062B VAL* 3.9 25.6 - - + +
1066B ARG* 5.9 4.3 - - - +
1089B ALA* 3.3 18.8 - - + +
1090B SER* 2.9 37.1 + - - +
1092B THR* 1.3 76.7 - - + +
1094B ARG* 1.3 60.4 + - - +
1096B VAL* 3.3 7.6 + - - +
1097B LEU* 2.9 37.1 + - - +
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Residues in contact with ARG1094 (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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1086B VAL* 3.4 20.8 + - + +
1087B THR 4.0 9.3 + - - -
1089B ALA* 3.4 28.8 + - + +
1090B SER 3.0 10.1 + - - +
1091B ARG* 3.5 30.6 + - - +
1093B GLU* 1.3 76.0 - - - +
1095B ALA* 1.3 63.7 + - - +
1097B LEU* 3.1 7.7 + - - +
1098B ILE* 3.0 34.7 + - + +
1131B VAL* 3.1 52.5 + - + +
1132B ALA* 4.3 4.5 - - - +
1133B GLU* 5.1 9.0 + - - +
1136B GLN* 5.3 1.6 - - - -
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Residues in contact with ALA1095 (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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1091B ARG 3.2 10.9 + - - +
1092B THR* 3.5 10.1 - - - +
1094B ARG* 1.3 79.5 - - - +
1096B VAL* 1.3 59.2 + - + +
1099B ASP* 2.9 17.0 + - - +
1133B GLU* 5.8 2.5 - - - +
1136B GLN* 2.8 42.3 + - - +
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Residues in contact with VAL1096 (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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1066B ARG* 3.0 50.5 - - - +
1092B THR* 2.9 31.8 + - + +
1093B GLU* 3.7 7.0 - - - +
1095B ALA* 1.3 79.5 - - + +
1097B LEU* 1.3 56.4 + - - +
1099B ASP* 3.7 6.0 - - - +
1100B GLU* 2.8 27.8 + - + +
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Residues in contact with LEU1097 (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* 3.9 19.1 - - + -
1065B ILE* 3.8 13.0 - - + -
1066B ARG* 3.6 27.1 - - + -
1069B VAL* 3.6 26.9 - - + +
1082B VAL* 6.5 0.2 - - + -
1085B CYS* 4.1 31.4 - - + +
1086B VAL* 4.6 8.3 - - + +
1089B ALA* 4.6 0.7 - - + -
1093B GLU 2.9 23.3 + - - +
1094B ARG* 3.6 4.5 - - - +
1096B VAL* 1.3 73.6 - - - +
1098B ILE* 1.3 65.4 + - + +
1100B GLU* 3.5 15.1 + - - +
1101B VAL* 3.7 7.8 + - - +
1128B MET* 3.3 20.0 - - + +
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Residues in contact with ILE1098 (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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1086B VAL* 4.9 2.9 - - + -
1094B ARG* 3.0 27.3 + - + +
1097B LEU* 1.3 76.2 - - + +
1099B ASP* 1.3 62.4 + - - +
1101B VAL* 3.6 2.8 + - - +
1102B CYS* 3.0 31.5 + - - -
1128B MET* 3.6 56.6 - - + +
1131B VAL* 4.3 1.8 - - + -
1132B ALA* 3.8 17.7 - - + +
1136B GLN* 3.4 26.5 - - + +
1140B VAL* 3.6 31.4 - - + -
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Residues in contact with ASP1099 (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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1095B ALA 2.9 19.8 + - - +
1096B VAL* 3.8 6.5 - - - +
1098B ILE* 1.3 77.0 - - - +
1100B GLU* 1.3 67.7 + - - +
1101B VAL 3.1 1.3 + - - -
1102B CYS* 4.4 5.2 - - - +
1103B THR* 3.1 46.6 + - - +
1136B GLN* 3.4 8.5 - - - +
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Residues in contact with GLU1100 (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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1066B ARG* 3.6 9.5 + - - +
1067B GLY* 2.7 50.0 + - - +
1069B VAL* 3.2 28.1 + - - +
1070B LEU 4.5 1.6 + - - -
1096B VAL* 2.8 17.8 + - + +
1097B LEU* 3.6 10.1 - - - +
1098B ILE 3.3 0.4 - - - -
1099B ASP* 1.3 81.3 + - - +
1101B VAL* 1.3 61.9 + - + +
1103B THR* 4.1 2.9 + - - -
1104B MET* 2.8 48.3 + - + +
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Residues in contact with VAL1101 (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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1069B VAL* 3.7 35.9 - - + -
1070B LEU* 4.2 7.9 - - + +
1097B LEU 3.7 5.3 + - - +
1098B ILE 3.6 7.3 + - - +
1099B ASP 3.1 0.4 - - - -
1100B GLU* 1.3 81.7 - - + +
1102B CYS* 1.3 63.7 + - - +
1103B THR 3.5 0.2 - - - -
1104B MET* 3.6 2.7 - - - +
1110B SER* 5.3 0.3 - - - -
1111B ALA* 3.4 23.1 + - + +
1112B LEU* 3.4 34.6 + - + +
1115B MET* 3.1 33.2 - - + -
1128B MET* 5.1 5.6 - - + -
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Residues in contact with CYS1102 (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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1098B ILE* 3.0 27.2 + - - +
1099B ASP* 3.1 9.4 + - - +
1101B VAL* 1.3 79.5 - - - +
1103B THR* 1.3 64.8 + - + +
1104B MET 4.5 1.5 - - - +
1112B LEU* 4.5 13.5 - - - -
1136B GLN* 5.5 1.8 - - - -
1139B ILE* 4.9 13.2 - - + -
1140B VAL* 3.8 38.1 - - - -
1143B LYS* 3.1 42.4 + - + -
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Residues in contact with THR1103 (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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1099B ASP* 3.1 41.4 + - - +
1100B GLU* 4.1 3.3 + - - -
1102B CYS* 1.3 79.6 - - + +
1104B MET* 1.3 69.8 + - - +
1105B ASN* 3.4 8.7 + - - +
1143B LYS* 5.2 1.6 - - - +
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Residues in contact with MET1104 (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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1067B GLY* 4.7 9.6 - - - +
1070B LEU* 4.4 21.8 - - - -
1100B GLU* 2.8 50.9 + - + +
1101B VAL* 3.6 3.6 - - - +
1102B CYS 3.6 1.6 - - - +
1103B THR* 1.3 82.8 + - - +
1105B ASN* 1.3 70.8 + - - +
1110B SER* 4.1 1.4 - - - -
1111B ALA* 2.9 39.8 + - + +
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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