Contacts of the helix formed by residues 1164 - 1176 (chain C) in PDB entry 5Y3R
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 CYS1164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1112C ALA* 4.8 9.9 - - + -
1113C LEU* 3.6 19.4 - - + +
1116C ALA* 4.7 4.5 - - + -
1119C LYS* 6.5 0.4 - - - -
1125C GLN* 3.5 11.9 - - - -
1162C SER 2.9 1.2 + - - -
1163C LEU* 1.3 74.6 - - - +
1165C LEU* 1.3 52.7 + - - +
1166C LEU* 2.6 19.4 + - - +
1167C ASP* 2.9 39.7 + - - +
1168C LEU* 3.7 6.2 + - - +
1256C TRP* 3.3 37.2 - - + -
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Residues in contact with LEU1165 (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 GLU* 4.6 9.2 - - + +
1113C LEU* 4.9 2.9 - - + -
1157C PHE* 3.0 32.5 - - + +
1158C PRO* 3.1 12.8 - - + +
1160C SER* 3.6 13.0 - - - +
1161C ALA* 3.0 25.6 - - - +
1162C SER* 3.0 31.2 + - - +
1163C LEU 3.1 1.6 - - - -
1164C CYS* 1.3 76.4 - - - +
1166C LEU* 1.3 52.0 + - - +
1167C ASP 3.3 0.2 - - - -
1168C LEU* 2.8 22.3 + - + +
1169C VAL* 2.1 53.1 + - + +
1260C LEU* 3.5 10.1 - - + -
1264C LEU* 4.9 0.9 - - + -
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Residues in contact with LEU1166 (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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1163C LEU 4.4 2.2 - - - +
1164C CYS 2.6 9.4 + - - +
1165C LEU* 1.3 74.0 - - - +
1167C ASP* 1.3 98.2 + - - +
1169C VAL* 3.0 11.4 + - - +
1170C LYS* 3.0 37.2 + - - +
1256C TRP* 3.5 31.2 - - + -
1259C LEU* 3.6 31.0 - - + +
1260C LEU* 3.3 14.1 - - + +
1263C ALA* 3.6 21.8 - - + -
1264C LEU 4.9 0.4 - - - +
1340C ARG* 3.8 17.9 - - - +
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Residues in contact with ASP1167 (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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1125C GLN* 2.2 45.2 + - - +
1129C ASP* 4.9 8.6 - - - +
1132C ASP* 5.5 0.7 - - - +
1164C CYS* 2.9 19.6 + - - +
1166C LEU* 1.3 97.0 - - - +
1168C LEU* 1.3 70.1 + - + +
1170C LYS* 4.7 4.3 + - - +
1171C TRP* 3.3 18.5 + - - +
1256C TRP* 5.1 1.0 - - - -
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Residues in contact with LEU1168 (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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1108C MET* 5.5 5.4 - - + +
1109C GLU* 4.4 17.7 - - + -
1112C ALA* 4.7 6.3 - - + -
1113C LEU* 3.8 29.2 - - + -
1128C CYS* 4.6 11.0 - - - -
1132C ASP* 4.2 20.4 - - - +
1164C CYS* 3.8 8.1 - - - +
1165C LEU* 2.8 24.1 + - + +
1167C ASP* 1.3 87.2 - - + +
1169C VAL* 1.3 62.0 + - + +
1171C TRP* 2.6 28.4 - - + +
1172C LEU* 2.8 16.9 + - + +
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Residues in contact with VAL1169 (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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1157C PHE 4.9 0.4 - - - +
1158C PRO* 4.1 13.5 - - + -
1165C LEU* 2.1 61.5 + - + +
1166C LEU* 3.0 5.6 + - - +
1168C LEU* 1.3 66.2 - - + +
1170C LYS* 1.3 60.9 + - + +
1172C LEU* 2.8 33.7 + - + +
1173C LEU* 5.4 1.1 - - + -
1260C LEU* 4.6 0.2 - - + -
1264C LEU* 3.6 36.8 - - + +
1267C TYR* 2.9 38.8 - - + -
1268C ASN* 5.2 1.1 - - - +
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Residues in contact with LYS1170 (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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1166C LEU* 3.0 39.3 + - - +
1167C ASP* 4.3 4.2 + - - +
1169C VAL* 1.3 76.3 - - + +
1171C TRP* 1.3 60.5 + - - +
1174C ALA* 4.2 5.0 - - - +
1263C ALA* 3.5 32.5 - - + +
1266C CYS* 5.4 2.7 - - + -
1267C TYR* 2.7 64.8 + - + +
1270C PHE* 5.9 2.0 - - + -
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Residues in contact with TRP1171 (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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1108C MET* 5.9 4.3 - - - -
1129C ASP* 5.8 1.8 - - + -
1132C ASP* 2.7 57.2 + - + +
1133C HIS* 5.1 0.6 - - - +
1134C LEU 4.5 0.7 - - - -
1135C CYS* 3.2 33.0 - - - -
1167C ASP 3.3 17.0 + - - +
1168C LEU* 2.6 20.3 - - + +
1170C LYS* 1.3 79.8 - - - +
1172C LEU* 1.3 79.9 + - + +
1174C ALA* 4.7 0.5 - - - +
1175C HIS* 3.4 29.1 + + + +
1176C CYS* 3.1 26.5 - - + -
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Residues in contact with LEU1172 (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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1154C PRO* 4.4 12.6 - - + -
1157C PHE* 4.0 26.7 - - + -
1158C PRO* 3.5 40.4 - - + -
1168C LEU* 2.8 20.6 + - + +
1169C VAL* 2.8 29.1 + - + +
1171C TRP* 1.3 91.4 - - + +
1173C LEU* 1.3 68.6 + - + +
1175C HIS 2.9 2.6 + - - -
1176C CYS* 2.3 38.7 + - + +
1177C GLY 3.8 1.6 - - - -
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Residues in contact with LEU1173 (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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1154C PRO* 4.9 12.1 - - + +
1158C PRO* 4.4 20.0 - - + -
1169C VAL* 4.9 0.9 - - + +
1172C LEU* 1.3 89.2 - - + +
1174C ALA* 1.3 67.8 + - - +
1177C GLY* 3.1 24.3 - - - +
1178C ARG 3.1 0.3 + - - -
1215C GLU* 2.7 39.6 - - + +
1220C LEU* 4.8 18.2 - - + -
1267C TYR* 2.6 29.9 + - + +
1268C ASN* 6.0 0.7 - - - +
1271C ILE* 4.2 18.8 - - + -
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Residues in contact with ALA1174 (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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1170C LYS 4.2 7.0 - - - +
1171C TRP 4.7 0.7 - - - +
1173C LEU* 1.3 72.5 - - - +
1175C HIS* 1.3 64.5 + - - +
1178C ARG* 3.1 17.3 + - - +
1215C GLU* 3.8 15.4 + - - +
1267C TYR* 2.1 33.8 + - + +
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Residues in contact with HIS1175 (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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1135C CYS* 2.9 29.2 + - + +
1136C ARG* 3.7 22.9 + - + -
1139C GLU* 2.6 39.8 + - - -
1141C LYS* 4.2 6.6 + - - -
1171C TRP* 3.4 28.6 + + + +
1172C LEU 2.9 5.1 + - - -
1174C ALA* 1.3 82.3 - - - +
1176C CYS* 1.3 65.9 + - - +
1178C ARG* 3.0 26.3 + - - +
1179C PRO* 3.2 5.0 - - - +
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Residues in contact with CYS1176 (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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1135C CYS* 3.5 9.4 - - - -
1139C GLU* 2.8 25.8 - - - +
1151C ARG* 5.6 5.7 - - - +
1154C PRO* 4.5 23.0 - - + +
1171C TRP* 3.1 35.9 - - + -
1172C LEU* 2.3 28.3 + - + +
1173C LEU* 4.9 0.2 - - - -
1175C HIS* 1.3 72.4 - - - +
1177C GLY* 1.3 63.5 + - - +
1178C ARG 3.0 1.3 - - - -
1179C PRO* 3.0 17.8 - - - +
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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