Contacts of the helix formed by residues 1214 - 1226 (chain A) in PDB entry 5ID6
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 SER1214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379A GLU* 3.4 20.6 - - - -
1210A LYS* 4.7 3.8 - - - -
1212A ALA 3.4 1.3 + - - -
1213A ILE* 1.3 75.1 - - - +
1215A ASN* 1.3 66.0 + - - +
1216A LYS* 3.5 6.9 + - - +
1217A GLU* 2.6 38.5 + - - +
1218A TRP* 2.8 23.6 + - - +
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Residues in contact with ASN1215 (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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379A GLU* 2.8 22.5 + - + +
999A TRP* 3.2 43.7 - - - +
1000A LEU* 3.3 29.8 - - + +
1057A ALA* 4.1 15.2 - - + +
1190A LYS* 4.9 2.8 + - - -
1214A SER* 1.3 72.0 - - - +
1216A LYS* 1.3 56.6 + - - +
1218A TRP* 3.7 5.4 - - - +
1219A LEU* 3.0 35.5 + - - +
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Residues in contact with LYS1216 (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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379A GLU* 3.8 5.2 + - + +
1056A ASP* 3.6 39.9 + - - +
1057A ALA* 3.8 20.0 + - + +
1058A ASP 4.2 10.1 + - - -
1059A TYR* 5.3 10.6 - - - +
1061A LYS* 5.0 2.4 - - - +
1214A SER* 3.0 7.5 + - - +
1215A ASN* 1.3 77.9 - - - +
1217A GLU* 1.3 65.1 + - + +
1220A GLU* 3.1 29.2 + - - +
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Residues in contact with GLU1217 (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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1193A TRP* 3.6 27.9 + - + +
1197A GLN* 4.7 3.3 + - - -
1210A LYS* 2.8 28.7 + - - +
1213A ILE* 3.4 13.2 - - + -
1214A SER* 2.6 43.7 + - - +
1216A LYS* 1.3 76.5 - - + +
1218A TRP* 1.3 57.2 + - - +
1220A GLU* 3.2 10.2 + - - +
1221A TYR* 2.9 31.0 + - - +
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Residues in contact with TRP1218 (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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1000A LEU* 2.9 38.8 + - + +
1004A ILE* 4.0 9.0 - - + +
1186A ASN* 3.5 46.4 - - + -
1189A ARG* 3.9 19.3 - - + -
1190A LYS* 3.4 43.7 - - + +
1213A ILE* 3.6 17.4 - - + +
1214A SER 2.8 15.8 + - - +
1215A ASN* 3.7 6.5 - - - +
1216A LYS 3.2 0.2 - - - -
1217A GLU* 1.3 75.8 - - - +
1219A LEU* 1.3 74.8 + - + +
1221A TYR* 3.1 27.4 + + - +
1222A ALA* 2.7 39.4 + - + +
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Residues in contact with LEU1219 (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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1000A LEU* 4.4 13.5 - - + -
1004A ILE* 4.1 14.8 - - + -
1011A VAL* 3.6 34.3 - - + -
1013A LEU* 4.6 5.2 - - + -
1057A ALA* 3.5 39.9 - - + +
1058A ASP* 4.1 7.9 - - - -
1059A TYR* 4.4 0.7 - - - -
1215A ASN 3.0 16.2 + - - +
1218A TRP* 1.3 98.2 - - + +
1220A GLU* 1.3 63.5 + - - +
1222A ALA* 4.3 2.0 - - + +
1223A GLN* 3.0 44.9 + - - +
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Residues in contact with GLU1220 (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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1059A TYR* 3.6 46.4 + - + +
1216A LYS* 3.1 24.1 + - + +
1217A GLU* 3.5 9.3 - - - +
1219A LEU* 1.3 77.3 - - - +
1221A TYR* 1.3 58.0 + - - +
1223A GLN 3.9 0.2 - - - -
1224A THR* 2.9 44.0 + - + +
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Residues in contact with TYR1221 (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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847A LYS* 5.4 5.0 - - - -
848A GLY* 5.4 0.9 - - - -
1189A ARG* 3.7 36.9 + - + +
1192A LEU* 3.4 27.6 - - - +
1193A TRP* 3.9 39.0 - + + -
1196A GLY* 6.6 0.2 - - - -
1217A GLU 2.9 16.9 + - - +
1218A TRP* 3.5 20.0 - + + +
1220A GLU* 1.3 74.5 - - - +
1222A ALA* 1.3 68.7 + - - +
1224A THR* 4.1 4.5 - - - -
1225A SER* 3.1 55.3 + - - -
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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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1004A ILE* 3.9 27.6 - - + -
1009A GLY* 4.0 11.1 + - - -
1189A ARG* 3.5 22.1 + - - +
1218A TRP* 2.7 36.6 + - + +
1219A LEU* 4.1 4.9 - - - +
1221A TYR* 1.3 77.2 - - - +
1223A GLN* 1.3 61.6 + - + +
1226A VAL* 3.5 16.3 + - - +
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Residues in contact with GLN1223 (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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1008A THR 3.4 16.6 - - - +
1009A GLY* 2.9 30.4 + - - +
1010A PHE* 4.6 0.6 - - - +
1011A VAL* 4.5 1.4 - - - +
1058A ASP* 2.7 24.1 + - - +
1059A TYR* 3.3 11.2 + - + +
1060A ILE* 3.0 47.9 + - + +
1063A TRP* 3.7 10.6 - - + -
1219A LEU* 3.0 33.5 + - - +
1220A GLU 4.2 1.1 - - - +
1222A ALA* 1.3 79.8 - - - +
1224A THR* 1.3 59.2 + - - +
1225A SER 3.6 0.2 - - - -
1226A VAL* 3.3 14.2 - - - +
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Residues in contact with THR1224 (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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1059A TYR* 3.5 36.8 - - + +
1060A ILE* 5.4 1.3 - - + -
1220A GLU* 2.9 28.3 + - + +
1221A TYR* 3.8 4.9 + - - -
1223A GLN* 1.3 77.5 - - - +
1225A SER* 1.3 66.1 + - - +
1226A VAL* 3.5 2.0 + - - -
1227A LYS* 3.8 9.0 + - - +
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Residues in contact with SER1225 (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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847A LYS* 5.5 2.8 - - - +
1189A ARG* 4.1 10.7 + - - -
1221A TYR* 3.1 49.9 + - - -
1224A THR* 1.3 76.1 + - - +
1226A VAL* 1.3 69.4 + - - +
1227A LYS* 3.1 7.2 + - - +
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Residues in contact with VAL1226 (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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1006A PRO 4.9 5.2 - - - +
1007A SER* 3.0 32.8 - - - +
1008A THR* 4.4 8.7 - - - +
1156A ASN* 5.9 2.0 - - + -
1157A SER* 5.8 0.4 - - - +
1189A ARG* 5.1 3.8 - - - +
1222A ALA 3.5 16.3 + - - +
1223A GLN* 3.3 27.1 - - - +
1225A SER* 1.3 77.5 + - - +
1227A LYS* 1.3 95.6 + - - +
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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