Contacts of the helix formed by residues 1076 - 1090 (chain A) in PDB entry 5WS3
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 ASP1076 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1041A PHE* 2.8 21.6 + - - +
1042A ASP* 4.4 2.0 - - - -
1043A ARG* 3.2 28.4 + - - +
1075A GLY* 1.3 67.6 - - - -
1077A PRO* 1.3 66.1 - - - +
1078A GLU* 2.9 37.2 + - - +
1079A LEU* 3.1 21.9 + - + +
1080A GLU* 2.8 28.9 + - - +
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Residues in contact with PRO1077 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075A GLY 3.0 9.3 - - - +
1076A ASP* 1.3 87.8 - - - +
1078A GLU* 1.3 58.6 + - + +
1080A GLU* 3.7 11.8 - - + +
1081A GLY* 2.9 23.7 + - - -
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Residues in contact with GLU1078 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043A ARG* 3.0 33.2 + - - +
1076A ASP* 2.9 11.8 + - - +
1077A PRO* 1.3 81.3 - - + +
1079A LEU* 1.3 57.3 + - - +
1081A GLY* 3.2 2.1 + - - -
1082A TRP* 2.9 27.7 + - + +
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Residues in contact with LEU1079 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041A PHE* 4.2 10.2 - - + -
1042A ASP 3.2 46.7 - - - +
1043A ARG* 3.5 35.9 - - + +
1048A VAL* 3.7 13.5 - - + -
1049A ASP* 4.4 10.3 - - + -
1052A LEU* 3.8 4.9 - - + +
1076A ASP* 3.1 23.8 + - + +
1078A GLU* 1.3 72.6 - - - +
1080A GLU* 1.3 60.8 + - - +
1082A TRP* 3.3 26.0 + - + +
1083A ALA* 2.9 30.0 + - - +
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Residues in contact with GLU1080 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041A PHE* 3.5 28.5 - - + -
1074A LYS* 3.8 8.7 - - - +
1075A GLY 3.0 33.5 + - - +
1076A ASP 2.8 19.8 + - - +
1077A PRO* 3.7 10.0 - - + +
1078A GLU 3.3 0.2 - - - -
1079A LEU* 1.3 72.9 - - - +
1081A GLY* 1.3 56.1 + - - +
1083A ALA* 3.3 1.6 + - - +
1084A ARG* 2.9 37.3 + - + +
1095A VAL* 5.5 0.3 - - - +
1097A THR* 3.8 23.7 - - + +
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Residues in contact with GLY1081 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077A PRO 2.9 15.7 + - - -
1078A GLU* 3.2 3.6 + - - -
1080A GLU* 1.3 76.1 - - - +
1082A TRP* 1.3 56.3 + - - +
1084A ARG* 3.4 6.8 + - - +
1085A SER* 2.8 30.0 + - - -
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Residues in contact with TRP1082 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043A ARG* 5.4 3.8 - - - -
1049A ASP* 4.0 13.9 - - + -
1052A LEU* 3.7 23.6 - - + -
1053A LYS* 3.8 36.3 - - + -
1056A GLU* 2.9 46.8 + - - +
1078A GLU* 2.9 17.1 + - + +
1079A LEU* 3.6 24.9 - - + +
1080A GLU 3.3 0.2 - - - -
1081A GLY* 1.3 76.0 - - - +
1083A ALA* 1.3 57.3 + - - +
1085A SER* 3.2 10.3 + - - -
1086A LEU* 3.0 33.8 + - + +
1089A LYS* 6.3 0.2 - - - -
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Residues in contact with ALA1083 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041A PHE* 4.4 12.1 - - + -
1052A LEU* 4.0 25.5 - - + +
1071A ILE* 5.1 1.8 - - + -
1079A LEU 2.9 17.0 + - - +
1080A GLU 3.7 3.6 - - - +
1082A TRP* 1.3 73.4 - - - +
1084A ARG* 1.3 61.7 + - - +
1086A LEU* 3.1 5.6 + - - +
1087A GLU 2.9 23.0 + - - -
1093A VAL* 4.9 0.2 - - - +
1095A VAL* 3.4 34.5 - - + +
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Residues in contact with ARG1084 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080A GLU* 2.9 24.3 + - + +
1081A GLY* 3.8 6.5 - - - +
1083A ALA* 1.3 75.3 - - - +
1085A SER* 1.3 56.8 + - - +
1087A GLU* 2.9 30.5 + - - +
1088A GLU* 2.9 31.3 + - - +
1095A VAL* 3.1 28.3 + - + +
1096A ILE* 4.6 0.4 - - - +
1097A THR* 2.6 46.1 + - - +
1098A GLU* 5.3 4.0 + - - +
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Residues in contact with SER1085 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081A GLY 2.8 18.6 + - - -
1082A TRP* 3.4 13.0 - - - -
1083A ALA 3.2 0.2 - - - -
1084A ARG* 1.3 77.6 - - - +
1086A LEU* 1.3 57.4 + - - +
1088A GLU* 3.5 11.2 + - - +
1089A LYS* 3.0 50.3 + - - +
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Residues in contact with LEU1086 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052A LEU* 3.8 43.5 - - + +
1055A ILE* 3.9 23.8 - - + -
1056A GLU* 3.9 25.4 - - + +
1071A ILE* 6.0 0.2 - - + -
1082A TRP* 3.0 22.5 + - + +
1083A ALA* 3.1 7.4 + - - +
1085A SER* 1.3 76.7 - - - +
1087A GLU* 1.3 57.0 + - - +
1089A LYS* 4.3 13.9 - - + +
1090A HIS* 2.9 52.8 + - + +
1093A VAL* 4.0 12.7 - - + +
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Residues in contact with GLU1087 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083A ALA 2.9 12.4 + - - +
1084A ARG* 2.9 42.9 + - - +
1086A LEU* 1.3 74.5 - - - +
1088A GLU* 1.3 65.4 + - - +
1090A HIS 2.8 21.0 - - - +
1091A GLY* 4.9 0.2 - - - -
1093A VAL* 3.2 25.3 - - - +
1094A LYS* 3.5 15.8 + - - +
1095A VAL* 3.3 30.5 + - + +
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Residues in contact with GLU1088 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084A ARG 2.9 17.6 + - - +
1085A SER* 3.8 9.2 - - - +
1087A GLU* 1.3 77.0 - - - +
1089A LYS* 1.3 61.9 + - - +
1090A HIS 5.2 0.3 - - - -
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Residues in contact with LYS1089 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056A GLU* 5.0 6.1 + - - -
1082A TRP* 6.3 0.2 - - - -
1085A SER* 3.0 38.3 + - - +
1086A LEU* 3.7 16.3 - - + +
1087A GLU 3.1 0.2 - - - -
1088A GLU* 1.3 79.3 - - - +
1090A HIS* 1.3 83.4 + - + +
1091A GLY 4.2 1.0 + - - -
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Residues in contact with HIS1090 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1055A ILE* 5.2 0.9 - - + -
1059A SER* 3.8 31.0 + - - -
1064A PHE* 3.4 21.6 - + - -
1065A GLN* 5.4 3.8 + - - -
1086A LEU* 2.9 39.9 + - + +
1087A GLU 2.8 19.3 + - - +
1088A GLU 5.1 0.2 - - - -
1089A LYS* 1.3 103.9 + - + +
1091A GLY* 1.3 61.8 + - - +
1092A ASN* 3.1 18.4 - - - +
1093A VAL* 3.3 19.9 + - + +
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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