Contacts of the helix formed by residues 1088 - 1105 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537D ALA* 6.2 3.4 - - + -
1084D VAL* 4.5 13.6 + - + -
1087D GLU* 1.3 91.5 - - + +
1089D THR* 1.3 64.3 + - - +
1090D GLY 3.2 3.1 - - - +
1091D LEU* 3.2 25.4 + - + +
1092D LYS* 3.7 7.9 + - + +
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Residues in contact with THR1089 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1008D ALA* 4.6 5.4 - - - +
1085D THR 3.3 25.1 + - - -
1086D VAL* 3.7 12.7 - - - -
1087D GLU 3.6 2.2 - - - -
1088D TRP* 1.3 80.6 - - - +
1090D GLY* 1.3 56.8 + - - +
1092D LYS* 3.7 4.7 + - - +
1093D VAL* 2.9 33.2 + - - +
1137D PRO* 5.8 4.3 - - - -
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Residues in contact with GLY1090 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533D LEU* 5.6 2.5 - - - +
536D PHE* 5.8 9.6 - - - +
1086D VAL 5.2 1.8 + - - -
1087D GLU 5.3 0.8 + - - -
1088D TRP* 3.2 1.8 - - - +
1089D THR* 1.3 78.1 - - - +
1091D LEU* 1.3 49.1 + - - +
1093D VAL* 4.3 5.3 - - - +
1094D ALA* 2.7 38.1 + - - +
1133D ASP* 5.6 8.6 - - - +
1137D PRO* 5.4 10.2 - - - +
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Residues in contact with LEU1091 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533D LEU* 5.3 14.1 - - + +
1088D TRP* 3.2 21.3 + - + +
1090D GLY* 1.3 76.1 - - - +
1092D LYS* 1.3 60.5 + - - +
1094D ALA* 3.1 4.9 + - - +
1095D LYS* 2.9 31.7 + - - +
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Residues in contact with LYS1092 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008D ALA* 4.2 16.8 - - + +
1088D TRP* 3.7 9.8 + - + +
1089D THR* 3.7 6.3 + - - +
1091D LEU* 1.3 76.0 - - - +
1093D VAL* 1.3 55.1 + - - +
1095D LYS* 4.7 1.8 - - - +
1096D ARG* 2.6 42.5 + - + +
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Residues in contact with VAL1093 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008D ALA* 3.8 19.9 - - + +
1089D THR* 2.9 23.0 + - - +
1090D GLY* 4.3 4.3 - - - -
1092D LYS* 1.3 76.5 - - - +
1094D ALA* 1.3 58.8 + - - +
1096D ARG* 4.5 0.2 - - - -
1097D LEU* 2.8 38.4 + - + +
1133D ASP* 6.2 4.0 - - + -
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Residues in contact with ALA1094 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529D GLU* 5.3 7.9 - - + +
533D LEU* 5.1 12.6 - - + -
1090D GLY 2.7 23.8 + - - +
1091D LEU* 3.1 7.3 + - - +
1093D VAL* 1.3 77.2 - - - +
1095D LYS* 1.3 56.2 + - - +
1098D HIS* 2.7 40.3 + - + +
1133D ASP* 5.7 10.1 - - + -
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Residues in contact with LYS1095 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091D LEU 2.9 14.5 + - - +
1092D LYS* 4.8 1.8 - - - +
1094D ALA* 1.3 75.6 - - - +
1096D ARG* 1.3 59.9 + - - +
1098D HIS* 4.8 1.1 - - - -
1099D ARG* 2.6 40.5 + - + +
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Residues in contact with ARG1096 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008D ALA* 4.7 14.1 - - - +
1092D LYS* 2.6 23.5 + - + +
1093D VAL* 4.5 1.8 - - - -
1095D LYS* 1.3 78.0 - - - +
1097D LEU* 1.3 55.0 + - - +
1100D SER* 2.6 40.1 + - - +
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Residues in contact with LEU1097 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093D VAL* 2.8 25.4 + - + +
1094D ALA* 5.1 0.2 - - - -
1096D ARG* 1.3 74.9 - - - +
1098D HIS* 1.3 54.6 + - - +
1100D SER* 4.8 0.4 - - - -
1101D LEU* 2.7 40.0 + - - +
1129D CYS* 5.3 5.6 - - - -
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Residues in contact with HIS1098 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D ARG* 5.9 6.7 - - + -
522D VAL* 5.9 1.7 - - - -
525D THR* 3.4 39.5 + - - -
526D ARG* 5.2 2.9 - - + -
529D GLU* 4.8 10.3 - - + -
1094D ALA* 2.7 23.6 + - + +
1095D LYS* 5.9 0.9 - - - -
1097D LEU* 1.3 76.4 - - - +
1099D ARG* 1.3 62.5 + - + +
1101D LEU* 4.1 1.5 - - - +
1102D LEU* 2.9 43.1 + - + +
1125D PHE* 4.8 11.6 - + - -
1129D CYS* 4.4 24.4 - - + +
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Residues in contact with ARG1099 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095D LYS* 2.6 29.0 + - + +
1098D HIS* 1.3 82.0 - - + +
1100D SER* 1.3 57.8 - - - +
1102D LEU* 4.3 2.9 - - - +
1103D ASN* 2.9 33.1 + - - +
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Residues in contact with SER1100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096D ARG* 2.6 25.2 + - - +
1097D LEU* 4.5 0.9 - - - -
1099D ARG* 1.3 78.4 - - - +
1101D LEU* 1.3 57.3 + - - +
1103D ASN* 4.3 2.9 - - - +
1104D ARG* 2.8 31.7 + - - +
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Residues in contact with LEU1101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097D LEU 2.7 23.2 + - - +
1098D HIS* 4.1 1.6 - - - +
1100D SER* 1.3 76.9 - - - +
1102D LEU* 1.3 59.5 + - - +
1104D ARG* 3.4 4.2 + - - +
1105D ILE* 2.9 31.9 + - - +
1125D PHE* 3.6 24.5 - - + -
1129D CYS* 5.5 2.7 - - - -
1318D LEU* 6.0 4.9 - - + -
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Residues in contact with LEU1102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522D VAL* 6.2 4.3 - - + -
1098D HIS* 2.9 30.9 + - + +
1099D ARG* 4.3 3.4 - - - +
1101D LEU* 1.3 77.2 - - - +
1103D ASN* 1.3 50.3 + - - +
1105D ILE* 3.8 2.4 - - - +
1106D ILE* 2.6 37.9 + - - +
1125D PHE* 4.3 16.1 - - + -
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Residues in contact with ASN1103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099D ARG 2.9 20.6 + - - +
1100D SER* 4.3 3.6 - - - +
1102D LEU* 1.3 75.9 - - - +
1104D ARG* 1.3 58.4 + - - +
1105D ILE 3.2 1.8 - - - -
1106D ILE* 3.9 5.4 - - - -
1107D LEU* 2.9 34.5 + - - +
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Residues in contact with ARG1104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100D SER 2.8 22.8 + - - +
1101D LEU* 3.9 5.4 - - - +
1103D ASN* 1.3 76.2 - - - +
1105D ILE* 1.3 58.2 + - - +
1107D LEU* 4.6 2.1 - - - +
1108D ALA* 4.4 12.0 + - - +
1319D LEU* 6.0 7.2 - - + -
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Residues in contact with ILE1105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101D LEU 2.9 17.0 + - - +
1102D LEU* 3.8 3.1 - - - +
1104D ARG* 1.3 75.1 - - - +
1106D ILE* 1.3 62.5 + - - +
1107D LEU 3.6 0.4 - - - -
1108D ALA* 3.9 16.7 - - - +
1113D PHE* 5.9 2.3 - - - +
1121D ILE* 6.3 3.1 - - + -
1125D PHE* 5.5 7.0 - - + -
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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