Contacts of the helix formed by residues 1210 - 1222 (chain A) in PDB entry 6A5T
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 THR1210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1204A MET* 3.3 18.7 - - - +
1209A LEU* 1.3 80.0 - - - +
1211A MET* 1.3 62.9 + - - +
1212A ASN* 2.8 10.7 + - + +
1213A GLN* 2.4 59.0 + - + +
1214A VAL* 3.4 15.4 - - - +
1233A ASP* 5.2 5.4 - - - -
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Residues in contact with MET1211 (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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1199A LEU* 3.7 24.5 - - + -
1204A MET* 3.7 15.5 - - + -
1210A THR* 1.3 73.6 - - - +
1212A ASN* 1.3 66.3 + - - +
1214A VAL* 3.4 2.8 + - - +
1215A ALA* 2.9 26.9 + - - +
1230A TRP* 3.5 25.6 - - + +
1231A SER 3.7 13.7 - - - +
1232A GLU 4.4 2.0 - - - +
1233A ASP* 4.0 16.0 + - - +
1238A LEU* 3.5 59.9 - - + -
1239A ILE 4.3 10.3 - - - +
1240A ILE* 4.5 7.4 - - - +
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Residues in contact with ASN1212 (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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1210A THR* 2.8 10.5 + - + +
1211A MET* 1.3 80.7 - - - +
1213A GLN* 1.3 65.4 + - + +
1215A ALA* 3.7 2.1 - - - +
1216A ASP* 2.8 54.8 + - - +
1230A TRP* 4.5 28.9 + - + -
1233A ASP* 5.0 1.5 + - - +
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Residues in contact with GLN1213 (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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1208A GLN 3.8 3.8 + - - +
1209A LEU* 3.2 35.1 - - + +
1210A THR* 2.4 40.1 + - + +
1212A ASN* 1.3 75.1 - - + +
1214A VAL* 1.3 59.9 + - + +
1216A ASP* 3.0 14.8 - - - +
1217A LYS* 2.9 35.7 + - + +
1277A ARG* 3.9 6.3 + - - +
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Residues in contact with VAL1214 (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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1145A LEU* 4.4 17.0 - - + -
1148A VAL* 6.1 0.7 - - + -
1199A LEU* 4.9 6.1 - - + -
1204A MET* 4.5 6.5 - - + -
1209A LEU* 4.4 24.7 - - + -
1210A THR 3.4 18.6 + - - +
1211A MET 3.4 2.5 + - - +
1212A ASN 3.2 0.8 - - - -
1213A GLN* 1.3 75.3 - - + +
1215A ALA* 1.3 61.9 + - - +
1217A LYS* 3.0 7.0 + - + +
1218A ILE* 2.9 39.9 + - + +
1240A ILE* 4.9 7.9 - - + -
1274A ILE* 5.0 0.4 - - + -
1276A LEU* 3.6 32.3 - - + -
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Residues in contact with ALA1215 (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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1211A MET 2.9 18.3 + - - +
1212A ASN* 3.7 3.4 - - - +
1214A VAL* 1.3 76.2 - - - +
1216A ASP* 1.3 63.6 + - - +
1218A ILE* 3.2 15.6 + - + +
1219A SER* 3.0 26.3 + - - -
1228A VAL* 3.8 16.6 - - + +
1230A TRP* 3.7 31.0 - - + +
1240A ILE* 5.3 5.0 - - + +
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Residues in contact with ASP1216 (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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1212A ASN* 2.8 48.1 + - - +
1213A GLN* 3.0 15.8 - - - +
1215A ALA* 1.3 77.6 - - - +
1217A LYS* 1.3 58.5 + - + +
1219A SER* 3.1 9.3 + - - +
1220A GLU* 2.9 34.6 + - - +
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Residues in contact with LYS1217 (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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1213A GLN* 2.9 24.1 + - + +
1214A VAL* 3.0 10.7 + - + +
1216A ASP* 1.3 79.0 - - - +
1218A ILE* 1.3 63.3 + - - +
1220A GLU* 3.1 40.1 + - + +
1221A VAL* 4.1 5.2 + - - +
1274A ILE* 5.1 6.8 - - + +
1275A ALA 4.5 13.2 - - - +
1276A LEU* 3.9 33.8 + - + +
1277A ARG* 6.1 0.2 - - - -
3E ASP* 5.7 2.8 + - - -
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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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1145A LEU* 5.4 6.1 - - + -
1197A LEU* 5.8 0.9 - - + -
1214A VAL* 2.9 23.2 + - + +
1215A ALA* 3.4 15.0 - - - +
1216A ASP 3.1 0.2 - - - -
1217A LYS* 1.3 76.7 - - - +
1219A SER* 1.3 60.8 + - - +
1220A GLU 3.0 1.5 + - - -
1221A VAL* 3.2 4.7 + - - +
1222A PHE* 2.8 53.2 + - + +
1226A LEU* 4.6 5.2 - - + -
1228A VAL* 4.0 21.1 - - + -
1240A ILE* 4.3 29.6 - - + -
1242A CYS* 5.2 2.5 - - - -
1270A MET* 5.1 12.3 - - + -
1274A ILE* 4.5 26.0 - - + -
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Residues in contact with SER1219 (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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1215A ALA 3.0 13.7 + - - -
1216A ASP* 3.1 6.9 + - - -
1218A ILE* 1.3 73.4 - - - +
1220A GLU* 1.3 65.0 + - - +
1221A VAL 3.2 0.8 + - - -
1222A PHE 3.7 13.7 + - - -
1223A SER* 3.6 21.6 + - - -
1228A VAL* 3.4 24.4 - - - +
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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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1216A ASP* 2.9 23.5 + - - +
1217A LYS* 3.1 44.2 + - + +
1218A ILE 3.0 0.2 - - - -
1219A SER* 1.3 79.0 - - - +
1221A VAL* 1.3 66.9 + - + +
1223A SER* 5.1 2.9 + - - -
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Residues in contact with VAL1221 (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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1217A LYS 4.8 4.9 - - - +
1218A ILE 3.2 4.4 + - - +
1220A GLU* 1.3 85.5 - - + +
1222A PHE* 1.3 84.5 + - + +
1223A SER* 3.4 7.4 + - - +
1225A ASP* 5.2 4.0 - - - +
1269A HIS* 6.0 0.2 - - + -
1273A LEU* 5.2 16.4 - - + -
1274A ILE* 5.1 8.3 - - + -
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Residues in contact with PHE1222 (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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1218A ILE* 2.8 38.5 + - + +
1219A SER* 3.9 10.7 + - - -
1221A VAL* 1.3 98.3 - - + +
1223A SER* 1.3 66.0 + - - +
1224A ASP 3.6 1.6 - - - -
1225A ASP* 4.3 14.8 - - + +
1226A LEU* 3.6 41.6 + - + +
1228A VAL* 4.8 0.2 - - - +
1266A ILE* 5.0 6.7 - - + -
1269A HIS* 4.1 25.6 - + - -
1270A MET* 3.5 32.8 - - + -
1273A LEU* 6.5 0.2 - - + -
1274A ILE* 4.1 15.3 - - + -
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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