Contacts of the helix formed by residues 1088 - 1105 (chain B) in PDB entry 5TWV
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 TRP1088 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537B ALA* 6.2 3.6 - - + -
1084B VAL* 4.5 13.4 + - + -
1087B GLU* 1.3 90.8 - - + +
1089B THR* 1.3 63.3 + - - +
1090B GLY 3.2 3.6 - - - +
1091B LEU* 3.2 25.6 + - + +
1092B LYS* 3.7 8.4 + - + +
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Residues in contact with THR1089 (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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1008B ALA* 4.6 5.1 - - - +
1085B THR 3.3 25.5 + - - -
1086B VAL* 3.7 12.2 - - - -
1087B GLU 3.6 3.0 - - - -
1088B TRP* 1.3 77.5 - - - +
1090B GLY* 1.3 57.6 + - - +
1091B LEU 3.2 0.2 - - - -
1092B LYS* 3.7 5.3 + - - +
1093B VAL* 2.9 33.0 + - - +
1137B PRO* 5.8 4.5 - - - -
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Residues in contact with GLY1090 (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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533B LEU* 5.6 1.9 - - - +
536B PHE* 5.8 10.4 - - - +
1086B VAL 5.2 2.2 + - - -
1087B GLU 5.3 0.4 + - - -
1088B TRP* 3.2 1.4 - - - +
1089B THR* 1.3 77.6 - - - +
1091B LEU* 1.3 50.9 + - - +
1093B VAL* 4.3 6.0 - - - +
1094B ALA* 2.7 38.6 + - - +
1133B ASP* 5.6 8.1 - - - +
1137B PRO* 5.4 11.2 - - - +
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Residues in contact with LEU1091 (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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533B LEU* 5.3 13.9 + - + +
1088B TRP* 3.2 20.7 + - + +
1090B GLY* 1.3 76.2 - - - +
1092B LYS* 1.3 60.1 + - - +
1094B ALA* 3.1 4.5 + - - +
1095B LYS* 2.9 31.5 + - - +
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Residues in contact with LYS1092 (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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1008B ALA* 4.2 17.0 - - + +
1088B TRP* 3.7 10.1 + - + +
1089B THR* 3.7 6.8 + - - +
1091B LEU* 1.3 77.0 - - - +
1093B VAL* 1.3 55.2 + - - +
1095B LYS* 4.7 2.0 - - - +
1096B ARG* 2.6 42.6 + - + +
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Residues in contact with VAL1093 (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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1008B ALA* 3.8 20.5 - - + +
1089B THR* 2.9 21.6 + - - +
1090B GLY* 4.3 4.7 - - - -
1092B LYS* 1.3 76.9 - - - +
1094B ALA* 1.3 59.2 + - - +
1096B ARG* 4.5 0.2 - - - -
1097B LEU* 2.8 38.2 + - + +
1133B ASP* 6.2 4.3 - - + -
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Residues in contact with ALA1094 (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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529B GLU* 5.3 7.4 - - + +
533B LEU* 5.1 12.6 - - + -
1090B GLY 2.7 23.1 + - - +
1091B LEU* 3.1 7.1 + - - +
1093B VAL* 1.3 77.2 - - - +
1095B LYS* 1.3 55.8 + - - +
1098B HIS* 2.7 39.8 + - - +
1133B ASP* 5.7 10.1 - - + -
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Residues in contact with LYS1095 (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 LEU 2.9 14.5 + - - +
1092B LYS* 4.8 2.0 - - - +
1094B ALA* 1.3 75.0 - - - +
1096B ARG* 1.3 60.5 + - - +
1098B HIS* 4.8 1.3 - - - -
1099B ARG* 2.6 40.8 + - + +
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Residues in contact with ARG1096 (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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1008B ALA* 4.7 13.7 - - - +
1092B LYS* 2.6 24.2 + - + +
1093B VAL* 4.5 1.8 - - - -
1095B LYS* 1.3 78.8 - - - +
1097B LEU* 1.3 54.5 + - - +
1100B SER* 2.6 39.7 + - - +
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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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1093B VAL* 2.8 25.0 + - + +
1096B ARG* 1.3 76.1 - - - +
1098B HIS* 1.3 53.9 + - - +
1100B SER* 4.8 0.7 - - - -
1101B LEU* 2.7 40.4 + - - +
1129B CYS* 5.3 4.7 - - - -
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Residues in contact with HIS1098 (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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495B ARG* 5.9 6.3 - - + -
522B VAL* 5.9 1.3 - - - -
525B THR* 3.4 39.1 + - - -
526B ARG* 5.2 2.9 - - + -
529B GLU* 4.8 11.0 - - + +
1094B ALA* 2.7 23.2 + - + +
1095B LYS* 5.9 1.1 - - - -
1097B LEU* 1.3 77.0 - - - +
1099B ARG* 1.3 62.7 + - + +
1101B LEU* 4.1 2.2 - - - +
1102B LEU* 2.9 42.7 + - + +
1125B PHE* 4.8 11.5 - + - -
1129B CYS* 4.4 22.9 - - + +
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Residues in contact with ARG1099 (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 LYS* 2.6 27.3 + - + +
1098B HIS* 1.3 80.6 - - + +
1100B SER* 1.3 60.9 + - - +
1102B LEU* 4.3 2.9 - - - +
1103B ASN* 2.9 32.7 + - - +
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Residues in contact with SER1100 (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 LYS 3.8 0.2 + - - -
1096B ARG* 2.6 25.9 + - - -
1097B LEU* 4.5 0.7 - - - -
1099B ARG* 1.3 77.5 - - - +
1101B LEU* 1.3 57.3 + - - +
1103B ASN* 4.6 2.9 - - - -
1104B ARG* 2.8 32.2 + - - +
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Residues in contact with LEU1101 (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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1097B LEU 2.7 23.8 + - - +
1098B HIS* 4.1 1.6 - - - +
1100B SER* 1.3 76.8 - - - +
1102B LEU* 1.3 60.5 + - - +
1104B ARG* 3.7 4.0 - - - +
1105B ILE* 2.9 32.1 + - - +
1125B PHE* 3.6 24.3 - - + -
1129B CYS* 5.5 2.2 - - - -
1318B LEU* 6.0 4.5 - - + -
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Residues in contact with LEU1102 (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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522B VAL* 6.2 4.7 - - + -
1098B HIS* 2.9 31.5 + - + +
1099B ARG* 4.3 3.1 - - - +
1101B LEU* 1.3 76.7 - - - +
1103B ASN* 1.3 50.5 + - - +
1105B ILE* 3.8 3.4 - - - +
1106B ILE* 2.6 37.6 + - - +
1125B PHE* 4.3 16.0 - - + -
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Residues in contact with ASN1103 (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 ARG 2.9 20.0 + - - +
1100B SER* 4.3 3.1 - - - +
1102B LEU* 1.3 75.9 - - - +
1104B ARG* 1.3 60.6 + - - +
1105B ILE 3.2 2.2 - - - -
1106B ILE* 3.9 5.4 - - - -
1107B LEU* 2.9 34.7 + - - +
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Residues in contact with ARG1104 (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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1100B SER 2.8 21.8 + - - +
1101B LEU* 3.4 5.1 + - - +
1103B ASN* 1.3 76.7 - - - +
1105B ILE* 1.3 57.6 + - - +
1107B LEU* 4.6 2.3 - - - +
1108B ALA* 4.4 11.8 + - - +
1319B LEU* 6.0 7.6 - - + -
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Residues in contact with ILE1105 (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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1101B LEU 2.9 16.8 + - - +
1102B LEU* 3.8 3.4 - - - +
1104B ARG* 1.3 76.0 - - - +
1106B ILE* 1.3 62.3 + - - +
1107B LEU 3.6 0.4 - - - -
1108B ALA* 3.9 17.1 - - - +
1113B PHE* 5.9 2.4 - - - +
1121B ILE* 6.3 2.9 - - + -
1125B PHE* 5.5 6.7 - - + -
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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