Contacts of the helix formed by residues 1088 - 1105 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537F ALA* 6.2 2.9 - - + -
1084F VAL* 4.5 14.3 + - + -
1087F GLU* 1.3 89.7 - - + +
1089F THR* 1.3 64.9 + - - +
1090F GLY 3.2 3.1 - - - +
1091F LEU* 3.2 26.1 + - + +
1092F LYS* 3.7 8.5 + - + +
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Residues in contact with THR1089 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008F ALA* 4.6 5.1 - - - +
1085F THR 3.3 24.2 + - - -
1086F VAL* 3.7 13.1 - - - -
1087F GLU 3.6 2.2 - - - -
1088F TRP* 1.3 81.0 - - - +
1090F GLY* 1.3 57.3 + - - +
1091F LEU 3.2 0.4 - - - -
1092F LYS* 4.1 4.8 - - - +
1093F VAL* 2.9 33.5 + - - +
1137F PRO* 5.8 4.3 - - - -
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Residues in contact with GLY1090 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533F LEU* 5.6 2.1 - - - +
536F PHE* 5.8 10.4 - - - +
1086F VAL 5.2 2.0 + - - -
1087F GLU 5.3 0.6 + - - -
1088F TRP* 3.2 1.8 - - - +
1089F THR* 1.3 77.6 - - - +
1091F LEU* 1.3 50.4 + - - +
1093F VAL* 4.3 5.8 - - - +
1094F ALA* 2.7 37.9 + - - +
1133F ASP* 5.6 7.9 - - - +
1137F PRO* 5.4 11.7 - - - +
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Residues in contact with LEU1091 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533F LEU* 5.3 13.7 + - + +
1088F TRP* 3.2 20.8 + - + +
1090F GLY* 1.3 76.3 - - - +
1092F LYS* 1.3 60.8 + - - +
1094F ALA* 3.1 4.6 + - - +
1095F LYS* 2.9 31.2 + - - +
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Residues in contact with LYS1092 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008F ALA* 4.2 16.4 - - + +
1088F TRP* 3.7 10.0 + - + +
1089F THR* 3.7 6.4 + - - +
1091F LEU* 1.3 75.5 - - - +
1093F VAL* 1.3 55.4 + - - +
1095F LYS* 4.7 2.5 - - - +
1096F ARG* 2.6 42.1 + - + +
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Residues in contact with VAL1093 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008F ALA* 3.8 20.3 - - + +
1089F THR* 2.9 22.6 + - - +
1090F GLY* 4.3 4.7 - - - -
1092F LYS* 1.3 75.2 - - - +
1094F ALA* 1.3 58.3 + - - +
1096F ARG* 4.5 0.2 - - - -
1097F LEU* 2.8 38.5 + - + +
1133F ASP* 6.2 4.7 - - + -
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Residues in contact with ALA1094 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529F GLU* 5.3 8.3 - - + +
533F LEU* 5.1 12.1 - - + -
1090F GLY 2.7 23.8 + - - +
1091F LEU* 3.1 6.7 + - - +
1093F VAL* 1.3 77.6 - - - +
1095F LYS* 1.3 55.8 + - - +
1098F HIS* 2.7 40.7 + - - +
1133F ASP* 5.7 9.2 - - + -
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Residues in contact with LYS1095 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091F LEU 2.9 14.3 + - - +
1092F LYS* 4.8 1.6 - - - +
1094F ALA* 1.3 74.4 - - - +
1096F ARG* 1.3 60.1 + - - +
1098F HIS* 4.8 0.9 - - - -
1099F ARG* 2.6 40.5 + - + +
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Residues in contact with ARG1096 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008F ALA* 4.7 14.4 - - - +
1092F LYS* 2.6 24.3 + - + +
1093F VAL* 4.5 1.6 - - - -
1095F LYS* 1.3 78.2 - - - +
1097F LEU* 1.3 54.3 + - - +
1100F SER* 2.6 40.1 + - - +
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Residues in contact with LEU1097 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093F VAL* 2.8 25.0 + - + +
1094F ALA* 5.1 0.2 - - - -
1096F ARG* 1.3 74.9 - - - +
1098F HIS* 1.3 55.1 + - - +
1100F SER* 4.8 0.7 - - - -
1101F LEU* 2.7 40.1 + - - +
1129F CYS* 5.3 5.2 - - - -
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Residues in contact with HIS1098 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495F ARG* 5.9 6.1 - - + -
522F VAL* 5.9 1.2 - - - -
525F THR* 3.4 39.1 + - - -
526F ARG* 5.2 2.5 - - - -
529F GLU* 4.8 10.8 - - + -
1094F ALA* 2.7 23.5 + - + +
1095F LYS* 5.9 0.9 - - - -
1097F LEU* 1.3 77.4 - - - +
1099F ARG* 1.3 61.6 + - + +
1101F LEU* 4.1 2.4 - - - +
1102F LEU* 2.9 43.3 + - + +
1125F PHE* 4.8 11.6 - + - -
1129F CYS* 4.4 23.3 - - + +
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Residues in contact with ARG1099 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095F LYS* 2.6 27.3 + - + +
1098F HIS* 1.3 81.0 - - + +
1100F SER* 1.3 60.3 + - - +
1102F LEU* 4.3 3.1 - - - +
1103F ASN* 2.9 33.4 + - - +
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Residues in contact with SER1100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096F ARG* 2.6 26.3 + - - -
1097F LEU* 4.8 0.4 - - - -
1099F ARG* 1.3 78.8 - - - +
1101F LEU* 1.3 58.0 + - - +
1103F ASN* 4.6 3.1 - - - -
1104F ARG* 2.8 31.5 + - - +
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Residues in contact with LEU1101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097F LEU 2.7 22.5 + - - +
1098F HIS* 4.1 1.8 - - - +
1100F SER* 1.3 76.6 - - - +
1102F LEU* 1.3 58.5 + - - +
1104F ARG* 3.7 4.1 - - - +
1105F ILE* 2.9 31.9 + - - +
1125F PHE* 3.6 24.5 - - + -
1129F CYS* 5.5 2.7 - - - -
1318F LEU* 6.0 4.5 - - + -
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Residues in contact with LEU1102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522F VAL* 6.2 4.5 - - + -
1098F HIS* 2.9 30.1 + - + +
1099F ARG* 4.3 2.9 - - - +
1101F LEU* 1.3 76.7 - - - +
1103F ASN* 1.3 49.8 + - - +
1105F ILE* 3.8 2.4 - - - -
1106F ILE* 2.6 37.8 + - - +
1125F PHE* 4.3 16.5 - - + -
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Residues in contact with ASN1103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099F ARG 2.9 19.8 + - - +
1100F SER* 4.3 3.6 - - - +
1102F LEU* 1.3 75.4 - - - +
1104F ARG* 1.3 59.0 + - - +
1105F ILE 3.2 2.0 - - - -
1106F ILE* 3.9 5.2 - - - -
1107F LEU* 2.9 34.7 + - - +
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Residues in contact with ARG1104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100F SER 2.8 22.8 + - - +
1101F LEU* 3.9 5.4 - - - +
1103F ASN* 1.3 75.8 - - - +
1105F ILE* 1.3 58.5 + - - +
1107F LEU* 5.2 2.0 - - - +
1108F ALA* 4.4 12.5 + - - +
1319F LEU* 6.0 7.9 - - + -
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Residues in contact with ILE1105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101F LEU 2.9 16.2 + - - +
1102F LEU* 4.6 3.1 - - - +
1104F ARG* 1.3 76.2 - - - +
1106F ILE* 1.3 63.0 + - - +
1107F LEU 3.6 0.4 - - - -
1108F ALA* 3.9 16.9 - - - +
1113F PHE* 5.9 2.3 - - - +
1121F ILE* 6.3 2.9 - - + -
1125F PHE* 5.5 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