Contacts of the helix formed by residues 1083 - 1092 (chain A) in PDB entry 5UNF
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 LYS1083 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1023A ALA* 5.5 0.2 - - - -
1078A LEU* 2.8 30.1 + - + +
1079A ALA* 4.5 1.3 + - - -
1081A GLU* 3.1 38.4 + - + +
1082A GLY* 1.3 76.0 - - - +
1084A VAL* 1.4 58.2 + - - +
1086A GLU* 3.4 37.0 - - + +
1087A ALA* 3.0 28.6 + - - +
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Residues in contact with VAL1084 (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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1020A ALA 4.8 0.4 - - - +
1021A ASP 4.2 15.7 - - - +
1022A ASN* 4.1 5.4 - - - +
1023A ALA* 3.6 32.8 - - + +
1026A VAL* 4.1 14.1 - - + -
1079A ALA* 5.9 0.7 - - - +
1082A GLY 3.6 7.0 + - - +
1083A LYS* 1.4 66.4 - - - +
1085A LYS* 1.4 71.4 + - + +
1086A GLU* 3.9 0.8 + - - -
1087A ALA* 3.1 6.9 + - - +
1088A GLN* 2.8 63.6 + - - +
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Residues in contact with LYS1085 (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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1021A ASP 4.8 7.3 + - - -
1084A VAL* 1.4 94.2 - - + +
1086A GLU* 1.4 64.6 + - - +
1088A GLN* 3.9 17.3 - - - +
1089A ALA* 3.1 27.2 + - - +
144B GLN* 5.6 5.6 - - - +
148B TYR* 5.9 11.7 + - + -
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Residues in contact with GLU1086 (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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1078A LEU* 3.4 24.7 - - + +
1083A LYS* 3.4 49.1 - - + +
1084A VAL 3.9 0.2 + - - -
1085A LYS* 1.4 82.1 + - - +
1087A ALA* 1.4 58.8 + - - +
1089A ALA* 3.3 8.0 + - - +
1090A ALA* 3.0 22.7 + - - +
150B PHE* 4.1 30.6 - - + -
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Residues in contact with ALA1087 (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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1026A VAL* 3.8 21.7 - - + +
1075A ALA* 3.6 25.2 - - - +
1078A LEU* 3.7 11.6 - - + +
1079A ALA* 3.9 5.8 - - - +
1083A LYS 3.0 19.5 + - - +
1084A VAL* 3.1 5.4 + - - +
1086A GLU* 1.4 72.1 - - - +
1088A GLN* 1.4 54.5 + - - +
1090A ALA* 3.3 3.3 + - - +
1091A ALA* 2.9 35.3 + - - +
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Residues in contact with GLN1088 (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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1017A ILE* 2.9 43.6 + - + +
1018A GLU* 4.4 9.5 + - - +
1020A ALA* 3.2 28.1 + - - +
1026A VAL* 4.3 3.1 - - + -
1084A VAL* 2.8 41.5 + - + +
1085A LYS* 3.9 21.8 - - - +
1087A ALA* 1.4 71.0 - - - +
1089A ALA* 1.4 60.0 + - - +
1091A ALA* 3.6 1.7 + - - +
1092A GLU* 3.0 31.9 + - - +
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Residues in contact with ALA1089 (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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1085A LYS 3.1 19.5 + - - +
1086A GLU* 3.5 8.1 - - - +
1087A ALA 3.3 0.2 - - - -
1088A GLN* 1.4 73.6 - - - +
1090A ALA* 1.4 62.8 + - - +
1092A GLU* 3.3 19.2 + - - +
1093A GLN* 3.8 10.2 + - - +
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Residues in contact with ALA1090 (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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1071A GLN* 4.7 8.1 - - - +
1074A ASP* 4.8 5.6 - - + -
1075A ALA* 4.1 17.5 - - + +
1078A LEU* 3.9 16.8 - - + -
1086A GLU 3.0 17.4 + - - +
1087A ALA 3.3 5.4 + - - +
1089A ALA* 1.4 74.6 - - - +
1091A ALA* 1.4 57.9 + - - +
1093A GLN* 3.2 35.6 + - - +
1094A LEU* 4.1 4.5 + - - +
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Residues in contact with ALA1091 (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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1014A LEU* 3.6 11.0 - - + +
1017A ILE* 3.8 36.8 - - + -
1030A LEU* 4.7 5.6 - - + -
1075A ALA* 4.4 2.9 - - + +
1087A ALA 2.9 17.3 + - - +
1088A GLN 3.8 6.5 - - - +
1089A ALA 3.3 0.2 - - - -
1090A ALA* 1.4 73.1 - - - +
1092A GLU* 1.3 64.3 + - - +
1093A GLN 3.2 0.7 - - - -
1094A LEU* 3.3 35.4 - - + +
1095A LYS* 4.3 1.4 + - - +
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Residues in contact with GLU1092 (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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206A GLN* 5.1 4.4 - - - +
1014A LEU* 6.0 0.9 - - - +
1017A ILE* 5.3 1.7 - - - +
1018A GLU* 3.7 22.9 - - - +
1088A GLN* 3.0 23.0 + - - +
1089A ALA* 3.5 14.1 - - - +
1090A ALA 3.2 1.0 - - - -
1091A ALA* 1.3 78.6 - - - +
1093A GLN* 1.4 61.1 + - - +
1094A LEU 3.2 0.7 - - - -
1095A LYS* 2.8 52.4 + - - +
1096A THR* 4.2 3.8 + - - -
158B TRP* 3.1 51.8 + - + +
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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