Contacts of the helix formed by residues 1216 - 1228 (chain B) in PDB entry 4DDG
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195B GLU* 5.4 3.3 - - - +
1203B PHE* 5.8 0.2 - - + -
1215B SER* 1.3 75.4 - - - +
1217B HIS* 1.3 79.4 + - - +
1218B ILE* 3.2 19.0 - - + +
1219B HIS* 3.0 34.8 + - + +
1220B ILE* 3.3 11.9 + - - +
1266B TYR* 4.7 5.1 + - - -
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Residues in contact with HIS1217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1216B ASP* 1.3 84.7 + - - +
1218B ILE* 1.3 66.6 + - + +
1220B ILE* 3.0 12.8 + - + +
1221B ILE* 3.0 50.0 + - + +
1249B PHE* 3.6 30.3 - + - -
1266B TYR* 5.0 1.0 + - - -
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Residues in contact with ILE1218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1183B LEU* 4.1 12.3 - - + -
1190B PHE* 4.0 27.4 - - + -
1193B PHE* 4.0 17.5 - - + +
1194B ILE* 3.8 31.0 - - + -
1195B GLU* 4.7 7.9 - - - +
1203B PHE* 3.9 21.8 - - + -
1216B ASP* 4.4 18.4 - - + +
1217B HIS* 1.3 76.9 - - + +
1219B HIS* 1.3 60.0 + - - +
1221B ILE* 3.5 6.1 + - - +
1222B ALA* 2.9 31.9 + - - +
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Residues in contact with HIS1219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092B PHE* 4.5 3.8 - - + -
1093B TYR* 2.9 31.0 - - + +
1176B ARG* 5.1 0.2 - - - -
1179B THR* 3.7 13.0 - - + +
1183B LEU* 5.3 1.3 - - + -
1203B PHE* 3.7 28.8 - + - -
1207B GLU* 2.9 28.8 + - + -
1208B VAL* 3.5 20.1 - - + +
1214B GLU 4.1 2.8 + - - -
1215B SER* 3.9 12.3 - - - -
1216B ASP* 3.0 41.0 + - + +
1218B ILE* 1.3 76.5 - - - +
1220B ILE* 1.3 56.0 + - - +
1222B ALA* 3.3 2.0 + - - +
1223B LEU* 2.9 32.1 + - - +
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Residues in contact with ILE1220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092B PHE* 3.5 40.1 - - + -
1096B PHE* 5.3 1.0 - - + -
1215B SER* 5.8 0.4 - - - +
1216B ASP 3.4 13.2 - - - +
1217B HIS* 3.0 12.7 + - + +
1219B HIS* 1.3 73.4 - - - +
1221B ILE* 1.3 66.1 + - - +
1223B LEU* 3.9 1.2 - - - +
1224B ALA* 2.9 26.6 + - + +
1231B ILE* 4.0 15.7 - - + -
1233B VAL* 4.6 11.4 - - + -
1249B PHE* 3.6 30.7 - - + -
1266B TYR* 3.3 31.2 - - + +
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Residues in contact with ILE1221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189B PHE* 5.5 4.5 - - + -
1190B PHE* 3.8 26.0 - - + -
1217B HIS* 3.0 45.2 + - + +
1218B ILE* 4.1 4.0 - - - +
1220B ILE* 1.3 75.6 - - - +
1222B ALA* 1.3 60.1 + - - +
1224B ALA* 3.7 4.1 - - - +
1225B GLN* 2.9 44.8 + - + +
1249B PHE* 3.5 42.4 - - + +
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Residues in contact with ALA1222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179B THR* 3.9 13.0 - - + +
1182B TYR* 3.7 18.9 - - + -
1183B LEU* 3.7 32.1 - - + -
1190B PHE* 4.6 1.6 - - + -
1218B ILE 2.9 19.9 + - - +
1219B HIS 3.6 3.6 - - - +
1220B ILE 3.2 0.2 - - - -
1221B ILE* 1.3 81.4 - - - +
1223B LEU* 1.3 58.1 + - - +
1226B ALA* 2.9 29.4 + - - +
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Residues in contact with LEU1223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092B PHE* 4.0 10.8 - - + -
1093B TYR* 3.9 27.1 - - + -
1096B PHE* 3.5 36.1 - - + -
1175B LEU* 3.7 29.4 - - + +
1178B LEU* 4.2 12.8 - - + -
1179B THR* 3.7 18.3 - - - +
1219B HIS 2.9 17.2 + - - +
1220B ILE 4.0 2.9 - - - +
1222B ALA* 1.3 73.0 - - - +
1224B ALA* 1.3 60.0 + - - +
1226B ALA* 3.1 4.9 + - + +
1227B LEU* 2.9 37.6 + - + +
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Residues in contact with ALA1224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096B PHE* 4.5 9.8 - - + -
1220B ILE* 2.9 20.9 + - + +
1221B ILE* 3.7 6.1 - - - +
1223B LEU* 1.3 78.1 - - - +
1225B GLN* 1.3 57.7 + - + +
1227B LEU 3.5 0.3 + - - -
1228B SER* 2.9 23.6 + - - -
1229B VAL* 3.0 37.7 + - + +
1231B ILE* 5.1 9.9 - - + -
1249B PHE* 4.8 12.1 - - + +
1250B PRO* 5.5 0.7 - - + -
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Residues in contact with GLN1225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182B TYR* 3.5 45.2 + - + -
1189B PHE* 5.5 8.7 - - - -
1190B PHE* 5.9 0.4 - - - -
1221B ILE* 2.9 33.6 + - + +
1224B ALA* 1.3 77.0 - - + +
1226B ALA* 1.3 63.0 + - - +
1228B SER* 3.5 12.6 + - - +
1249B PHE 5.8 3.1 - - - +
1250B PRO* 6.6 0.7 - - + -
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Residues in contact with ALA1226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117B VAL* 4.1 13.9 - - - +
1121B SER* 6.0 1.9 - - - -
1178B LEU* 4.2 25.1 - - + +
1182B TYR* 3.8 24.4 - - + -
1185B ARG* 5.5 4.6 + - - +
1222B ALA 2.9 18.9 + - - +
1223B LEU* 3.1 11.6 + - + +
1225B GLN* 1.3 80.2 - - - +
1227B LEU* 1.3 61.4 + - + +
1228B SER* 3.3 0.7 + - - -
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Residues in contact with LEU1227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096B PHE* 3.7 30.5 - - + -
1113B ARG* 4.4 1.2 + - - -
1114B PHE* 3.9 36.8 - - + -
1117B VAL* 4.0 18.5 - - + +
1118B SER* 4.9 11.0 - - - -
1121B SER* 5.9 1.1 - - - +
1142B PHE* 4.5 8.1 - - + -
1175B LEU* 4.2 9.9 - - + -
1178B LEU* 3.7 26.2 - - + -
1223B LEU* 2.9 20.7 + - + +
1226B ALA* 1.3 77.6 - - - +
1228B SER* 1.3 75.0 + - - +
1229B VAL* 3.5 19.0 - - + +
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Residues in contact with SER1228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113B ARG* 3.1 32.8 + - - -
1117B VAL* 4.6 10.8 - - - +
1224B ALA 2.9 10.3 + - - -
1225B GLN* 3.5 10.4 + - - +
1226B ALA 3.3 3.8 - - - -
1227B LEU* 1.3 86.5 + - - +
1229B VAL* 1.3 56.8 + - - +
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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