Contacts of the helix formed by residues 1216 - 1228 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1195A GLU* 5.4 3.5 - - - +
1203A PHE* 5.8 0.4 - - + -
1215A SER* 1.3 73.9 - - - +
1217A HIS* 1.3 79.8 + - - +
1218A ILE* 3.2 19.2 - - + +
1219A HIS* 3.0 35.4 + - + +
1220A ILE* 3.3 12.4 + - - +
1266A TYR* 4.7 4.7 - - - -
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Residues in contact with HIS1217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1216A ASP* 1.3 86.0 + - - +
1218A ILE* 1.3 64.5 + - + +
1220A ILE* 3.0 12.8 + - + +
1221A ILE* 3.0 44.4 + - + +
1249A PHE* 3.6 29.2 - + - -
1266A TYR* 5.0 1.2 + - - -
8D LEU* 3.5 35.8 - - + +
9D THR* 5.2 3.8 - - + -
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Residues in contact with ILE1218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183A LEU* 4.1 12.1 - - + -
1190A PHE* 4.0 26.0 - - + -
1193A PHE* 4.0 14.8 - - + +
1194A ILE* 3.8 32.5 - - + -
1195A GLU* 4.7 7.9 - - - +
1203A PHE* 3.9 20.4 - - + -
1216A ASP* 4.4 19.7 - - + +
1217A HIS* 1.3 74.8 - - + +
1219A HIS* 1.3 61.9 + - - +
1221A ILE* 3.5 2.4 + - - +
1222A ALA* 2.9 32.0 + - - +
8D LEU* 3.8 19.0 - - + +
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Residues in contact with HIS1219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092A PHE* 4.5 4.4 - - + -
1093A TYR* 2.9 30.7 - - + +
1176A ARG* 5.1 0.2 - - - -
1179A THR* 3.7 13.1 - - + +
1183A LEU* 5.3 1.8 - - + +
1203A PHE* 3.7 28.9 - + - -
1207A GLU* 2.9 28.7 + - + -
1208A VAL* 3.5 19.7 - - + +
1214A GLU 4.1 3.0 + - - -
1215A SER* 3.9 13.0 - - - -
1216A ASP* 3.0 40.0 + - + +
1218A ILE* 1.3 76.4 - - - +
1220A ILE* 1.3 56.3 + - - +
1222A ALA* 3.3 1.8 + - - +
1223A LEU* 2.9 31.9 + - - +
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Residues in contact with ILE1220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092A PHE* 3.5 40.1 - - + -
1096A PHE* 5.3 1.0 - - + -
1215A SER* 5.8 0.4 - - - +
1216A ASP 3.4 13.5 - - - +
1217A HIS* 3.0 14.2 + - + +
1219A HIS* 1.3 73.5 - - - +
1221A ILE* 1.3 66.1 + - - +
1223A LEU* 3.9 1.0 - - - +
1224A ALA* 2.9 27.4 + - + +
1231A ILE* 4.0 15.7 - - + -
1233A VAL* 4.6 10.5 - - + -
1249A PHE* 3.6 30.1 - - + -
1266A TYR* 3.3 32.1 - - + +
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Residues in contact with ILE1221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189A PHE* 5.5 1.1 - - + -
1190A PHE* 3.8 26.5 - - + -
1217A HIS* 3.0 42.1 + - + +
1218A ILE 4.1 1.3 - - - +
1220A ILE* 1.3 75.7 - - - +
1222A ALA* 1.3 60.2 + - - +
1224A ALA* 3.7 4.3 - - - +
1225A GLN* 2.9 44.6 + - + +
1249A PHE* 3.5 41.5 - - + +
8D LEU* 3.9 34.5 - - + +
9D THR* 4.7 2.2 - - + +
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Residues in contact with ALA1222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179A THR* 3.9 13.9 - - + +
1182A TYR* 3.7 19.1 - - + +
1183A LEU* 3.7 32.3 - - + -
1190A PHE* 4.6 1.8 - - + -
1218A ILE 2.9 19.5 + - - +
1219A HIS 3.6 3.4 - - - +
1221A ILE* 1.3 81.7 - - - +
1223A LEU* 1.3 57.7 + - - +
1225A GLN 3.5 0.2 + - - -
1226A ALA* 2.9 29.2 + - - +
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Residues in contact with LEU1223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092A PHE* 4.0 11.2 - - + -
1093A TYR* 3.9 27.4 - - + -
1096A PHE* 3.5 35.0 - - + -
1175A LEU* 3.7 30.5 - - + +
1178A LEU* 4.2 12.8 - - + -
1179A THR* 3.7 18.5 - - - +
1219A HIS 2.9 17.6 + - - +
1220A ILE 4.0 2.7 - - - +
1222A ALA* 1.3 72.9 - - - +
1224A ALA* 1.3 60.1 + - - +
1226A ALA* 3.1 4.8 + - + +
1227A LEU* 2.9 37.7 + - + +
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Residues in contact with ALA1224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096A PHE* 4.5 9.6 - - + -
1220A ILE* 2.9 20.0 + - + +
1221A ILE* 3.7 6.7 - - - +
1223A LEU* 1.3 78.3 - - - +
1225A GLN* 1.3 58.4 + - + +
1227A LEU 3.7 0.3 - - - -
1228A SER* 2.9 22.9 + - - -
1229A VAL* 3.0 38.9 + - + +
1231A ILE* 5.1 10.1 - - + -
1249A PHE* 4.8 11.7 - - + +
1250A PRO* 5.5 0.4 - - + -
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Residues in contact with GLN1225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182A TYR* 3.5 45.5 + - + -
1189A PHE* 5.5 8.5 - - - -
1190A PHE* 5.9 0.8 - - - -
1221A ILE* 2.9 32.6 + - + +
1224A ALA* 1.3 77.0 - - + +
1226A ALA* 1.3 63.4 + - - +
1228A SER* 3.5 11.9 + - - +
1249A PHE 5.8 2.9 - - - +
1250A PRO* 6.6 0.7 - - + -
8D LEU 5.6 2.6 + - - -
9D THR 5.5 4.9 + - - -
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Residues in contact with ALA1226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117A VAL* 4.1 14.0 - - - +
1121A SER* 6.0 1.9 - - - -
1178A LEU* 4.2 25.6 - - + +
1182A TYR* 3.8 23.8 - - + -
1185A ARG* 5.5 5.3 + - - +
1222A ALA 2.9 18.7 + - - +
1223A LEU* 3.1 11.9 + - + +
1225A GLN* 1.3 79.2 - - - +
1227A LEU* 1.3 62.1 + - + +
1228A SER* 3.3 0.9 + - - -
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Residues in contact with LEU1227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096A PHE* 3.6 30.3 - - + -
1113A ARG* 4.4 1.4 + - - -
1114A PHE* 3.9 35.5 - - + -
1117A VAL* 4.0 17.7 - - + +
1118A SER* 4.9 11.0 - - - -
1121A SER* 5.9 1.3 - - - +
1142A PHE* 4.5 8.1 - - + -
1175A LEU* 4.2 9.9 - - + -
1178A LEU* 3.7 26.7 - - + -
1223A LEU* 2.9 19.2 + - + +
1226A ALA* 1.3 78.2 - - - +
1228A SER* 1.3 75.1 + - - +
1229A VAL* 3.5 20.0 - - + +
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Residues in contact with SER1228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113A ARG* 3.1 34.0 + - - -
1117A VAL* 4.6 10.9 - - - +
1224A ALA 2.9 10.9 + - - -
1225A GLN* 3.5 10.3 + - - +
1226A ALA 3.3 4.7 - - - -
1227A LEU* 1.3 85.4 + - - +
1229A VAL* 1.3 56.4 + - - +
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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