Contacts of the helix formed by residues 1081 - 1089 (chain C) in PDB entry 5UHA
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 ALA1081 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1076C MET* 3.3 13.7 + - - +
1079C TYR* 3.6 1.4 - - + +
1080C GLY* 1.3 75.3 - - - +
1082C ALA* 1.3 58.8 + - - +
1084C THR* 4.0 6.1 - - - -
1085C LEU* 3.0 18.6 + - - +
554D GLU* 2.8 45.4 - - + +
558D LEU* 4.0 7.8 - - + +
559D MET* 4.0 25.1 - - - -
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Residues in contact with ALA1082 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080C GLY 2.9 7.7 + - - -
1081C ALA* 1.3 70.3 - - - +
1083C TYR* 1.3 53.2 + - + +
1085C LEU* 3.2 7.9 + - - +
1086C GLN* 2.7 36.0 + - - +
554D GLU* 3.2 2.2 + - - -
1257D LEU* 4.0 7.0 - - + +
1258D ILE* 3.6 42.5 + - + +
1260D ALA 4.1 2.0 - - - +
1262D THR* 3.6 11.4 - - - +
1263D GLY* 3.9 16.4 - - - +
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Residues in contact with TYR1083 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082C ALA* 1.3 72.4 - - - +
1084C THR* 1.3 55.3 + - - +
1086C GLN* 3.2 11.1 + - - +
1087C GLU* 2.8 32.2 + - - +
548D SER* 4.9 3.8 + - - +
550D GLU* 3.8 36.2 + - + -
551D ALA* 4.8 2.9 - - - +
554D GLU* 2.8 30.4 + - - +
1257D LEU* 3.4 33.4 - - + +
1262D THR* 3.6 21.3 - - - -
1268D ARG* 3.4 24.7 + - + +
55E ILE* 3.5 30.3 - - + +
59E LYS* 5.8 2.6 - - - -
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Residues in contact with THR1084 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076C MET* 4.1 17.9 - - - -
1081C ALA* 3.3 9.1 - - + +
1083C TYR* 1.3 70.8 - - - +
1085C LEU* 1.3 63.8 + - - +
1087C GLU* 3.2 5.8 + - - +
1088C LEU* 2.9 40.4 + - + +
497D LEU* 4.4 17.5 - - + -
546D PRO* 5.3 4.3 - - + -
551D ALA* 3.3 37.3 + - + +
554D GLU* 2.5 30.3 + - - +
555D ALA* 4.9 1.1 + - + +
559D MET* 5.5 2.0 - - - -
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Residues in contact with LEU1085 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068C PHE* 4.5 4.9 - - + -
1073C CYS* 4.0 26.5 - - + +
1076C MET* 4.0 28.0 - - + +
1077C GLN* 3.7 22.2 - - + +
1081C ALA 3.0 11.5 + - - +
1082C ALA* 3.2 9.6 - - - +
1084C THR* 1.3 76.4 - - - +
1086C GLN* 1.3 64.3 + - - +
1088C LEU* 3.0 17.0 + - + +
1089C LEU* 3.2 21.9 + - + +
1252D VAL* 4.0 10.8 - - + -
1258D ILE* 3.6 33.7 - - + -
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Residues in contact with GLN1086 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082C ALA 2.7 20.0 + - - +
1083C TYR* 3.5 12.4 - - - +
1085C LEU* 1.3 72.8 - - - +
1087C GLU* 1.3 58.6 + - - +
1089C LEU* 3.1 11.5 + - - -
1090C THR* 2.3 33.4 + - + +
1114C GLU* 5.5 3.4 - - - +
1115C PRO* 3.6 37.6 + - - +
5D ASN* 5.8 3.0 - - - +
1255D GLY* 3.3 30.8 + - - +
1256D LYS* 4.8 2.4 - - - +
1257D LEU* 3.4 36.0 - - + +
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Residues in contact with GLU1087 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083C TYR 2.8 16.6 + - - +
1084C THR* 3.4 5.2 - - - +
1086C GLN* 1.3 78.3 + - - +
1088C LEU* 1.3 70.4 + - - +
1090C THR* 3.3 10.5 + - - -
1091C ILE* 3.4 25.4 + - + +
1092C LYS* 3.1 54.9 + - + +
1115C PRO* 5.1 1.1 - - + -
546D PRO* 4.0 4.3 - - - +
547D LEU* 3.2 16.2 + - - +
548D SER* 2.8 42.6 + - - +
551D ALA* 3.6 6.6 - - - +
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Residues in contact with LEU1088 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068C PHE* 3.5 50.0 - - + -
1076C MET* 4.9 2.0 - - + -
1084C THR* 2.9 31.9 + - + +
1085C LEU* 3.0 8.5 + - - +
1087C GLU* 1.3 84.7 - - - +
1089C LEU* 1.3 65.9 + - + +
1090C THR 3.5 2.1 + - - -
1092C LYS* 3.3 46.7 - - + +
1093C SER* 3.8 6.1 - - - -
422D VAL* 3.3 27.4 - - + +
497D LEU* 5.5 3.1 - - + -
544D HIS* 4.8 8.7 - - + +
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Residues in contact with LEU1089 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068C PHE* 4.4 13.2 - - + +
1073C CYS* 3.8 18.8 - - - -
1085C LEU* 3.2 20.8 + - + +
1086C GLN* 3.1 5.3 + - - +
1088C LEU* 1.3 87.2 - - + +
1090C THR* 1.3 66.7 + - + +
1093C SER* 4.3 1.3 - - - -
1094C ASP* 4.3 1.6 - - - +
1118C PRO* 4.2 4.3 - - - +
417D LEU 4.3 5.8 - - - +
419D GLY 5.0 0.7 - - - +
420D LYS* 2.9 71.8 + - + +
422D VAL* 5.1 0.2 - - + -
1252D VAL* 3.7 34.3 - - + +
1255D GLY* 5.6 1.7 - - - -
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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