Contacts of the helix formed by residues 1216 - 1228 (chain C) in PDB entry 4DDI
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 ASP1216 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1203C PHE* 5.9 2.0 - - + -
1214C GLU 5.6 0.2 - - - +
1215C SER* 1.3 74.7 - - - +
1217C HIS* 1.3 82.4 + - - +
1218C ILE* 3.3 9.7 + - + +
1219C HIS* 3.2 26.6 + - + +
1220C ILE* 3.2 23.0 - - - +
1266C TYR* 4.8 3.1 - - - -
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Residues in contact with HIS1217 (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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1216C ASP* 1.3 87.1 + - - +
1218C ILE* 1.3 65.3 + - + +
1220C ILE* 3.1 12.6 + - + +
1221C ILE* 3.0 36.6 + - + +
1249C PHE* 3.4 41.4 - + - -
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Residues in contact with ILE1218 (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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1183C LEU* 3.9 25.1 - - + -
1190C PHE* 4.2 14.6 - - + -
1193C PHE* 4.1 28.7 - - + +
1194C ILE* 3.8 27.4 - - + -
1195C GLU 5.4 1.1 - - - +
1203C PHE* 4.6 19.1 - - + -
1216C ASP* 3.3 7.5 - - + +
1217C HIS* 1.3 77.3 - - + +
1219C HIS* 1.3 64.4 + - + +
1221C ILE* 3.5 7.0 + - - +
1222C ALA* 2.9 29.5 + - - +
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Residues in contact with HIS1219 (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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1092C PHE* 4.4 5.2 - - + -
1093C TYR* 2.9 27.2 + - - +
1176C ARG* 4.9 0.7 - - - -
1179C THR* 4.0 7.6 + - - +
1183C LEU* 5.7 2.9 - - + -
1203C PHE* 3.7 26.4 - + - -
1207C GLU* 2.9 30.9 + - - +
1208C VAL* 3.6 19.1 - - + +
1214C GLU 3.7 12.4 + - - -
1215C SER* 3.9 8.9 - - - -
1216C ASP* 3.2 37.7 + - + +
1217C HIS 3.2 0.2 - - - -
1218C ILE* 1.3 77.5 - - + +
1220C ILE* 1.3 57.1 + - - +
1222C ALA* 3.4 5.7 + - - +
1223C LEU* 3.0 31.2 + - - +
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Residues in contact with ILE1220 (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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1092C PHE* 3.5 36.0 - - + -
1096C PHE* 4.8 1.7 - - + -
1215C SER* 5.6 0.2 - - - -
1216C ASP 3.2 16.6 - - - +
1217C HIS* 3.1 13.8 + - + +
1219C HIS* 1.3 72.1 - - - +
1221C ILE* 1.3 62.1 + - - +
1223C LEU* 3.5 1.4 + - - +
1224C ALA* 2.9 32.3 + - - +
1231C ILE* 3.7 29.8 - - + -
1233C VAL* 5.0 11.4 - - + -
1249C PHE* 4.9 5.6 - - + -
1259C LEU* 6.5 0.4 - - + -
1266C TYR* 3.2 39.3 - - + +
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Residues in contact with ILE1221 (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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1189C PHE* 5.9 4.0 - - + -
1190C PHE* 4.5 17.7 - - + -
1217C HIS* 3.0 36.3 + - + +
1218C ILE* 4.0 5.8 - - - +
1220C ILE* 1.3 76.1 - - - +
1222C ALA* 1.3 61.6 + - - +
1224C ALA* 3.3 2.7 + - + +
1225C GLN* 2.9 46.9 + - + +
1249C PHE* 3.9 32.5 - - + -
1250C PRO* 4.3 19.3 - - + -
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Residues in contact with ALA1222 (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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1179C THR* 4.2 9.2 - - - +
1182C TYR* 3.5 21.1 - - + -
1183C LEU* 3.7 32.3 - - + -
1190C PHE* 4.5 1.1 - - + -
1218C ILE 2.9 19.9 + - - +
1219C HIS* 3.5 5.8 - - - +
1221C ILE* 1.3 79.7 - - - +
1223C LEU* 1.3 58.2 + - - +
1225C GLN 3.5 0.2 + - - -
1226C ALA* 2.9 29.8 + - - +
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Residues in contact with LEU1223 (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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1092C PHE* 4.4 2.5 - - + -
1093C TYR* 3.9 19.5 - - + -
1096C PHE* 3.5 40.4 - - + -
1175C LEU* 3.8 27.1 - - + +
1178C LEU* 5.3 0.4 - - + -
1179C THR* 3.5 33.1 - - + +
1219C HIS 3.0 13.0 + - - +
1220C ILE 4.1 2.5 - - - +
1222C ALA* 1.3 74.6 - - - +
1224C ALA* 1.3 64.6 + - - +
1226C ALA* 3.1 7.2 + - - +
1227C LEU* 3.0 47.1 + - + +
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Residues in contact with ALA1224 (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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1096C PHE* 4.5 5.3 - - + -
1220C ILE 2.9 20.8 + - - +
1221C ILE* 3.7 6.3 - - - +
1222C ALA 3.3 0.2 - - - -
1223C LEU* 1.3 77.8 - - - +
1225C GLN* 1.3 57.2 + - - +
1227C LEU 3.6 0.2 + - - -
1228C SER 2.9 21.8 + - - -
1229C VAL* 3.0 36.5 + - - +
1231C ILE* 4.3 19.7 - - + -
1249C PHE* 4.6 1.6 - - + +
1250C PRO* 4.5 10.9 - - + +
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Residues in contact with GLN1225 (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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1182C TYR* 3.4 39.2 + - + +
1189C PHE* 4.3 22.6 - - - -
1190C PHE* 6.3 0.2 - - - -
1221C ILE* 2.9 34.1 + - + +
1224C ALA* 1.3 73.9 - - - +
1226C ALA* 1.3 67.0 + - - +
1228C SER* 3.2 14.4 + - - +
1250C PRO* 4.1 27.5 - - + +
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Residues in contact with ALA1226 (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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1117C VAL* 4.3 11.4 - - - +
1178C LEU* 4.2 13.2 - - + +
1182C TYR* 3.6 28.5 - - + -
1185C ARG* 5.5 7.6 + - - +
1222C ALA 2.9 19.3 + - - +
1223C LEU* 3.1 11.2 + - - +
1225C GLN* 1.3 78.4 - - - +
1227C LEU* 1.3 69.1 + - + +
1228C SER* 3.6 0.9 + - - -
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Residues in contact with LEU1227 (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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1096C PHE* 5.8 2.7 - - + -
1100C HIS* 6.3 0.2 - - + -
1113C ARG* 3.5 12.8 + - - -
1114C PHE* 3.5 38.5 - - + -
1117C VAL* 4.7 14.8 - - + +
1118C SER* 5.6 0.7 - - - +
1142C PHE* 4.4 13.0 - - + -
1175C LEU* 5.0 4.7 - - + -
1178C LEU* 4.0 24.7 - - + -
1223C LEU* 3.0 39.6 + - + +
1226C ALA* 1.3 85.4 - - + +
1228C SER* 1.3 75.8 + - - +
1229C VAL* 3.6 14.9 - - + +
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Residues in contact with SER1228 (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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1110C GLU* 4.7 1.9 - - - +
1113C ARG* 2.9 27.4 + - - -
1117C VAL* 4.8 3.6 - - - +
1224C ALA 2.9 9.2 + - - -
1225C GLN* 3.2 14.3 + - - +
1226C ALA 5.0 1.1 - - - -
1227C LEU* 1.3 88.3 + - - +
1229C VAL* 1.3 59.2 + - - +
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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