Contacts of the helix formed by residues 1074 - 1092 (chain Z) in PDB entry 5WTI
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 ALA1074 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1056Z LEU* 6.0 7.6 - - + -
1057Z MET 3.8 11.0 - - - +
1058Z LEU* 4.1 5.8 - - + +
1059Z TYR* 4.2 0.4 - - - -
1073Z MET* 1.3 75.7 - - - +
1075Z ALA* 1.3 58.3 + - - +
1076Z GLY 3.5 2.2 - - - +
1077Z VAL* 3.8 16.1 - - + +
1078Z PHE* 2.6 38.2 + - - +
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Residues in contact with ALA1075 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056Z LEU* 6.6 0.2 - - + -
1057Z MET* 4.0 4.4 + - + +
1059Z TYR* 3.6 35.0 - - + +
1074Z ALA* 1.3 73.5 - - - +
1076Z GLY* 1.3 64.4 + - - +
1079Z PHE* 3.1 37.6 + - + +
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Residues in contact with GLY1076 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074Z ALA* 3.5 2.2 - - - +
1075Z ALA* 1.3 78.5 - - - +
1077Z VAL* 1.3 59.2 + - - +
1079Z PHE* 5.4 0.7 - - - -
1080Z GLY* 3.1 23.8 + - - -
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Residues in contact with VAL1077 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071Z LYS* 6.3 0.4 - - - -
1073Z MET* 3.6 29.1 - - + +
1074Z ALA* 3.2 18.1 + - + +
1075Z ALA 3.2 0.4 - - - -
1076Z GLY* 1.3 78.7 - - - +
1078Z PHE* 1.3 67.1 + - - +
1081Z LYS* 3.0 42.1 + - + +
1084Z ARG* 6.0 1.8 - - - +
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Residues in contact with PHE1078 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881Z PHE* 4.5 7.6 - + - -
888Z PRO* 3.4 29.6 - - + -
1059Z TYR* 3.5 28.7 - - + -
1060Z ARG* 3.1 38.8 - - - -
1067Z PHE* 3.5 22.9 - + - -
1073Z MET* 3.6 32.8 - - + -
1074Z ALA 2.6 22.3 + - - +
1075Z ALA 4.0 2.0 - - - +
1077Z VAL* 1.3 74.4 - - - +
1079Z PHE* 1.3 85.1 + + - +
1082Z LEU* 3.1 29.5 + - + +
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Residues in contact with PHE1079 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877Z PHE* 4.0 24.0 - + - -
880Z ARG* 4.0 31.6 - - + -
881Z PHE* 5.5 5.4 - + - -
888Z PRO* 6.1 0.4 - - + -
1059Z TYR* 4.2 30.1 - + - -
1075Z ALA* 3.1 28.6 + - + +
1076Z GLY* 5.3 0.7 - - - -
1078Z PHE* 1.3 101.1 - + - +
1080Z GLY* 1.3 61.3 + - - +
1082Z LEU* 3.8 18.5 - - + +
1083Z GLU* 3.0 30.7 + - - +
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Residues in contact with GLY1080 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076Z GLY 3.1 21.3 + - - -
1079Z PHE* 1.3 78.8 - - - +
1081Z LYS* 1.3 60.0 + - - +
1083Z GLU* 3.8 5.6 - - - +
1084Z ARG* 3.1 47.8 + - - +
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Residues in contact with LYS1081 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067Z PHE* 4.1 15.3 - - + -
1071Z LYS* 6.4 0.2 - - - +
1073Z MET* 5.0 7.4 - - - -
1077Z VAL* 3.0 33.5 + - + +
1080Z GLY* 1.3 72.2 - - - +
1082Z LEU* 1.3 60.8 + - - +
1084Z ARG* 3.2 23.3 + - - +
1085Z ILE* 2.8 35.9 + - + +
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Residues in contact with LEU1082 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888Z PRO* 3.6 39.5 - - + +
889Z GLY 4.0 16.4 - - - +
890Z ILE* 4.4 5.8 - - + -
1066Z VAL* 4.5 10.1 - - + -
1067Z PHE* 3.6 16.4 - - + -
1078Z PHE* 3.1 21.0 + - + +
1079Z PHE* 3.8 26.0 - - + +
1081Z LYS* 1.3 78.6 - - - +
1083Z GLU* 1.3 61.5 + - - +
1085Z ILE* 3.2 3.9 - - - +
1086Z LEU* 3.1 54.5 + - + +
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Residues in contact with GLU1083 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890Z ILE* 4.2 25.1 - - + +
930Z PRO* 5.2 5.6 - - - +
932Z LYS* 5.2 9.7 - - - +
1079Z PHE 3.0 18.9 + - - +
1080Z GLY* 3.8 6.5 - - - +
1082Z LEU* 1.3 77.7 - - - +
1084Z ARG* 1.3 62.1 + - + +
1086Z LEU 3.2 0.3 + - - -
1087Z ILE* 2.8 53.8 + - + +
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Residues in contact with ARG1084 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076Z GLY 5.8 0.2 + - - -
1077Z VAL* 5.3 1.4 + - - +
1080Z GLY* 3.1 38.3 + - - +
1081Z LYS* 3.7 35.2 - - - +
1083Z GLU* 1.3 82.5 - - + +
1085Z ILE* 1.3 58.3 + - - +
1087Z ILE* 4.1 12.8 - - + +
1088Z SER* 3.1 24.9 + - - -
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Residues in contact with ILE1085 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940Z LEU* 4.9 7.2 - - + -
944Z ARG* 3.7 27.8 - - - +
1066Z VAL* 4.2 11.9 - - + +
1067Z PHE* 4.5 12.1 - - + -
1081Z LYS 2.8 22.2 + - - +
1082Z LEU* 3.2 18.6 - - + +
1084Z ARG* 1.3 76.3 - - - +
1086Z LEU* 1.3 69.3 + - + +
1088Z SER* 3.6 5.2 + - - -
1089Z LYS* 3.2 35.7 + - + +
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Residues in contact with LEU1086 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888Z PRO 4.6 0.2 - - - +
889Z GLY* 3.6 31.0 - - - -
890Z ILE* 3.7 25.6 - - + +
938Z ILE* 3.7 22.0 - - + +
939Z SER* 4.4 8.3 - - - -
940Z LEU* 4.6 11.2 - - + -
946Z LEU* 4.5 4.5 - - + +
1066Z VAL* 3.9 19.3 - - + -
1082Z LEU* 3.1 33.5 + - + +
1083Z GLU 3.8 2.2 - - - +
1085Z ILE* 1.3 86.4 - - + +
1087Z ILE* 1.3 60.3 + - - +
1088Z SER 3.1 1.6 - - - -
1089Z LYS* 3.3 7.1 + - - +
1090Z LEU* 3.0 27.0 + - - +
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Residues in contact with ILE1087 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890Z ILE* 3.7 25.1 - - + -
930Z PRO* 4.3 21.3 - - + -
1083Z GLU* 2.8 38.4 + - + +
1084Z ARG* 4.1 15.7 - - + +
1086Z LEU* 1.3 71.9 - - - +
1088Z SER* 1.3 60.6 + - - +
1090Z LEU* 3.8 12.2 - - + +
1091Z THR* 2.9 31.4 + - - +
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Residues in contact with SER1088 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084Z ARG 3.1 19.2 + - - -
1085Z ILE* 3.7 7.9 - - - -
1086Z LEU 3.1 0.8 - - - -
1087Z ILE* 1.3 80.1 - - - +
1089Z LYS* 1.3 64.1 + - - +
1091Z THR* 3.4 7.4 - - - +
1092Z ASN* 3.3 35.0 + - - +
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Residues in contact with LYS1089 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940Z LEU* 4.2 19.5 - - + +
944Z ARG* 3.6 43.2 - - - +
945Z LYS* 5.9 0.2 - - - -
946Z LEU* 3.7 26.9 - - + +
1085Z ILE* 3.2 20.5 + - + +
1086Z LEU* 3.3 5.6 + - - +
1088Z SER* 1.3 79.7 - - - +
1090Z LEU* 1.3 61.7 + - - +
1092Z ASN* 3.6 16.9 + - - +
1093Z GLN* 4.2 3.3 + - - +
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Residues in contact with LEU1090 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892Z CYS* 4.3 10.3 - - - -
928Z LEU* 3.3 52.3 - - + +
930Z PRO* 4.7 9.6 - - + -
938Z ILE* 4.1 19.1 - - + -
946Z LEU* 4.2 21.1 - - + +
1086Z LEU 3.0 16.9 + - - +
1087Z ILE* 4.1 9.9 - - + +
1088Z SER 3.2 0.2 - - - -
1089Z LYS* 1.3 74.5 - - - +
1091Z THR* 1.3 62.5 + - - +
1092Z ASN 3.1 4.7 - - - -
1093Z GLN* 3.1 23.4 + - + +
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Residues in contact with THR1091 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087Z ILE* 2.9 22.1 + - + +
1088Z SER* 3.4 14.1 - - - +
1090Z LEU* 1.3 77.8 - - - +
1092Z ASN* 1.3 67.9 + - - +
1093Z GLN 3.2 8.8 + - - +
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Residues in contact with ASN1092 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088Z SER* 3.3 24.3 + - - +
1089Z LYS* 3.9 9.8 - - - +
1090Z LEU 3.1 2.4 - - - -
1091Z THR* 1.3 87.9 - - - +
1093Z GLN* 1.3 57.1 + - - +
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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