Contacts of the helix formed by residues 1114 - 1124 (chain C) in PDB entry 1UKJ
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 TYR1114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1090C MET* 3.9 2.5 - - - -
1113C LEU* 1.3 70.0 - - - +
1115C GLY* 1.3 72.8 + - - +
1116C CYS* 3.7 20.8 - - + -
1117C THR* 2.9 44.1 + - + +
1118C PHE 3.0 8.8 + - - -
1157C GLU* 2.6 20.9 + - - +
1161C ASN* 6.6 0.4 - - - -
1211C LLP 3.2 65.0 + + + +
1400C SO4 3.5 36.7 + - - -
1559D TYR* 4.4 4.9 - - - -
1561D ARG* 2.6 27.4 + - - -
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Residues in contact with GLY1115 (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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1113C LEU 3.3 5.2 + - - -
1114C TYR* 1.3 78.0 - - - +
1116C CYS* 1.3 61.3 + - - +
1118C PHE* 3.5 7.5 + - - +
1119C ALA* 3.2 21.1 + - - +
1367C TYR* 4.7 9.6 + - - -
1740D LYS* 5.7 0.4 - - - -
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Residues in contact with CYS1116 (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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1090C MET* 3.4 19.8 - - + +
1114C TYR* 2.9 19.5 + - + -
1115C GLY* 1.3 69.8 - - - +
1117C THR* 1.3 57.4 + - - +
1118C PHE 3.0 1.6 - - - -
1119C ALA* 3.1 3.4 + - - +
1120C PHE* 2.7 35.5 + - - +
1561D ARG* 3.4 31.6 - - - +
1562D ILE* 5.3 2.7 - - - -
1740D LYS* 3.6 21.1 - - - +
1741D ASP* 4.0 13.6 - - - +
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Residues in contact with THR1117 (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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1090C MET* 3.3 14.1 - - - +
1093C ILE* 3.6 20.1 - - + +
1113C LEU* 4.2 5.0 - - - +
1114C TYR* 3.1 46.0 - - + +
1116C CYS* 1.3 75.5 - - - +
1118C PHE* 1.3 55.8 + - - +
1120C PHE* 3.5 2.9 - - - +
1121C LEU* 3.0 37.2 + - - +
1155C TYR* 3.8 25.6 - - - +
1157C GLU* 4.1 4.3 - - - +
1211C LLP 4.9 3.6 - - + +
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Residues in contact with PHE1118 (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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1111C ASN 5.8 1.8 - - - -
1113C LEU* 4.4 21.8 - - + +
1114C TYR 3.0 10.6 + - - +
1115C GLY 3.6 9.6 - - - +
1117C THR* 1.3 77.0 + - - +
1119C ALA* 1.3 62.8 + - + +
1121C LEU* 3.1 4.4 + - - -
1122C HIS* 2.8 82.8 + + + -
1123C HIS* 4.9 7.6 - - - -
1134C HIS* 3.9 17.7 - + - -
1367C TYR* 3.5 39.7 - + - +
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Residues in contact with ALA1119 (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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1115C GLY 3.2 11.9 + - - +
1116C CYS* 3.1 8.6 + - - +
1118C PHE* 1.3 84.5 - - + +
1120C PHE* 1.3 54.7 + - - +
1123C HIS* 2.7 54.2 + - + +
1124C GLY 3.6 0.2 + - - -
1740D LYS* 5.1 2.9 - - - +
1741D ASP* 3.6 23.9 - - - +
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Residues in contact with PHE1120 (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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1090C MET* 4.1 0.9 - - + -
1093C ILE* 3.5 19.3 - - + -
1094C THR* 3.8 30.7 - - + -
1097C LEU* 3.6 30.1 - - + -
1098C TRP* 3.9 26.2 - + - -
1116C CYS 2.7 19.4 + - - +
1117C THR* 3.5 7.2 - - - +
1118C PHE 3.1 0.2 - - - -
1119C ALA* 1.3 72.8 - - - +
1121C LEU* 1.3 58.0 + - - +
1124C GLY* 2.6 36.1 + - - +
1125C ILE* 3.3 29.8 + - + -
1741D ASP* 3.2 33.4 - - - +
1742D MET* 3.7 14.6 - - + -
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Residues in contact with LEU1121 (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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1097C LEU* 3.5 17.3 - - + -
1107C VAL* 4.6 4.3 - - + -
1109C LEU* 3.1 39.0 - - + -
1113C LEU* 3.4 20.9 - - + -
1117C THR* 3.0 24.5 + - - +
1118C PHE* 3.6 3.8 - - - +
1120C PHE* 1.3 83.3 - - + +
1122C HIS* 1.3 65.4 + - + +
1125C ILE* 3.2 34.1 - - + -
1126C GLY* 2.9 31.0 + - - -
1132C LEU* 3.8 15.8 - - + +
1155C TYR* 4.8 3.1 - - + -
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Residues in contact with HIS1122 (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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1109C LEU* 4.3 6.7 - - + +
1118C PHE* 2.8 55.0 + + + +
1121C LEU* 1.3 84.9 - - + +
1123C HIS* 1.3 76.5 + - + +
1124C GLY 3.6 0.2 - - - -
1126C GLY* 4.8 2.3 - - - -
1127C GLU* 3.8 14.4 + - - +
1132C LEU* 5.0 17.4 - - + +
1134C HIS* 2.8 40.5 + + - -
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Residues in contact with HIS1123 (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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1118C PHE* 4.9 8.2 - + - -
1119C ALA* 2.7 35.8 + - + +
1122C HIS* 1.3 91.8 + - + +
1124C GLY* 1.3 56.2 + - - +
1127C GLU* 3.7 18.4 + - - +
1602D ARG* 2.8 30.1 + - - -
1737D GLN* 6.6 0.4 - - + -
1741D ASP* 5.4 3.8 - - - +
1742D MET* 4.7 2.7 - - - +
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Residues in contact with GLY1124 (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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1119C ALA 3.6 0.2 + - - -
1120C PHE* 2.6 19.5 + - - -
1122C HIS 3.6 0.6 - - - -
1123C HIS* 1.3 74.6 - - - +
1125C ILE* 1.3 68.1 + - - -
1127C GLU* 2.8 15.6 + - - +
1128C PHE* 3.0 17.0 - - - -
1742D MET* 3.6 26.7 - - - -
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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