Contacts of the helix formed by residues 1201 - 1217 (chain A) in PDB entry 5A31
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 HIS1201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1169A ALA* 4.5 14.5 - - + +
1170A ASN* 4.0 32.6 + - - +
1199A LYS* 3.3 15.1 + - + +
1200A GLY* 1.3 73.3 - - - +
1202A GLU* 1.3 67.1 - - + +
1203A MET* 3.5 27.4 + - + -
1204A THR* 2.7 41.4 + - + +
1205A SER* 3.2 10.0 + - - -
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Residues in contact with GLU1202 (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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1134A TRP* 4.8 1.9 + - - -
1200A GLY 3.3 6.5 + - - +
1201A HIS* 1.3 75.8 - - + +
1203A MET* 1.3 74.7 + - + +
1205A SER* 3.4 9.9 + - - -
1206A ILE* 3.3 28.1 + - - +
1246A PRO* 3.9 24.8 - - + +
1248A ASN* 3.0 35.0 + - - +
1249A VAL* 3.3 18.2 - - - +
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Residues in contact with MET1203 (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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1133A SER* 4.1 8.1 - - - +
1134A TRP* 3.1 64.8 - - + +
1137A PHE* 3.5 27.3 - - + -
1170A ASN* 3.3 30.3 - - - +
1173A ALA* 3.6 11.5 - - + +
1201A HIS* 3.3 17.6 + - + -
1202A GLU* 1.3 87.5 - - + +
1204A THR* 1.3 58.8 + - - +
1206A ILE* 3.1 11.0 + - - +
1207A GLY 2.9 23.7 + - - -
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Residues in contact with THR1204 (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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1169A ALA* 4.5 7.9 - - + +
1172A TYR* 4.8 11.0 - - + -
1173A ALA* 3.5 26.9 - - + +
1176A LEU* 5.9 4.6 - - + +
1196A TYR* 4.0 31.8 + - + -
1199A LYS* 5.4 0.5 - - - +
1201A HIS* 2.7 39.4 + - + +
1203A MET* 1.3 73.8 - - - +
1205A SER* 1.3 59.4 + - - +
1207A GLY 4.3 0.2 - - - +
1208A LEU* 2.8 38.3 + - - +
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Residues in contact with SER1205 (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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1196A TYR 4.9 0.4 + - - -
1197A LEU* 4.1 35.6 + - - +
1200A GLY* 4.6 3.5 - - - -
1201A HIS 3.2 12.2 + - - -
1202A GLU* 3.4 10.8 - - - -
1203A MET 3.2 0.4 - - - -
1204A THR* 1.3 78.8 + - - +
1206A ILE* 1.3 59.2 + - - +
1208A LEU* 4.0 0.5 - - - +
1209A LEU* 3.0 34.6 + - - +
1231A HIS* 5.0 3.8 - - - -
1249A VAL* 3.9 21.8 - - - -
91R TYR* 5.0 2.6 + - - -
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Residues in contact with ILE1206 (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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1134A TRP* 4.1 16.2 - - + -
1137A PHE* 4.4 6.3 - - + -
1202A GLU* 3.3 37.2 + - - +
1203A MET* 3.1 13.7 + - - +
1205A SER* 1.3 74.9 - - - +
1207A GLY* 1.3 66.4 + - - +
1209A LEU* 3.5 1.6 + - - +
1210A LEU* 3.2 30.6 + - + +
1248A ASN* 3.9 21.1 - - - +
1249A VAL* 4.0 16.4 - - - -
1252A ALA* 4.1 15.7 - - + +
1603A LEU* 4.6 4.5 - - + -
1605A ALA* 4.0 26.7 - - + -
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Residues in contact with GLY1207 (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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1137A PHE* 4.1 6.5 - - - -
1173A ALA 3.9 9.4 - - - -
1177A MET* 3.2 36.5 - - - +
1203A MET 2.9 13.6 + - - -
1204A THR 3.7 1.3 - - - -
1206A ILE* 1.3 76.6 - - - +
1208A LEU* 1.3 65.5 + - - +
1210A LEU* 4.0 0.2 - - - -
1211A GLY* 2.9 19.8 + - - -
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Residues in contact with LEU1208 (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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1173A ALA 5.0 0.4 + - - -
1176A LEU* 3.7 32.8 - - + +
1185A LEU* 4.0 6.7 - - + -
1188A LEU* 4.3 3.8 - - + -
1193A ILE* 4.3 20.2 - - + +
1196A TYR* 3.5 35.7 - - + -
1197A LEU* 4.0 25.8 - - + +
1204A THR* 2.8 24.2 + - - +
1205A SER 4.0 2.9 - - - +
1207A GLY* 1.3 71.2 - - - +
1209A LEU* 1.3 60.7 + - + +
1211A GLY* 5.0 0.9 - - - -
1212A VAL* 2.7 54.0 + - + +
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Residues in contact with LEU1209 (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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1197A LEU* 4.1 17.5 - - + -
1205A SER 3.0 18.6 + - - +
1206A ILE 4.0 3.4 - - - +
1207A GLY 3.1 0.2 - - - -
1208A LEU* 1.3 80.3 - - + +
1210A LEU* 1.3 59.6 + - - +
1212A VAL* 4.5 2.2 - - + -
1213A SER* 2.5 34.2 + - - -
1227A LEU* 4.4 21.8 - - + -
1228A LEU* 3.9 20.2 - - + -
1231A HIS* 3.8 26.7 - - + +
1249A VAL* 4.2 7.4 - - + +
1252A ALA* 4.8 2.2 - - + -
1253A ALA* 3.8 37.2 - - + +
1256A GLY* 5.4 1.6 - - - -
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Residues in contact with LEU1210 (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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1177A MET* 3.9 17.9 - - + -
1181A LEU* 4.2 4.8 - - + +
1206A ILE* 3.2 21.4 + - + +
1209A LEU* 1.3 76.4 - - - +
1211A GLY* 1.3 58.1 + - - +
1213A SER* 3.9 2.9 - - - -
1214A ALA* 2.9 32.1 + - - +
1252A ALA* 3.9 27.6 - - + +
1255A VAL* 4.1 20.0 - - + -
1256A GLY* 4.4 1.3 - - - +
1259A LEU* 4.3 15.8 - - + +
1603A LEU* 4.7 7.4 - - + -
1605A ALA* 3.9 28.0 - - + -
1606A LEU* 4.4 14.4 - - + +
1609A LEU* 4.8 4.9 - - + -
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Residues in contact with GLY1211 (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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1177A MET* 3.8 12.2 + - - -
1180A GLY* 3.1 32.3 - - - -
1181A LEU* 4.8 0.2 - - - -
1185A LEU* 4.1 4.5 - - - -
1207A GLY 2.9 17.6 + - - -
1208A LEU 3.7 0.2 - - - -
1210A LEU* 1.3 75.4 - - - +
1212A VAL* 1.3 65.5 + - - +
1214A ALA* 3.2 1.7 + - - -
1215A ALA* 3.1 19.2 + - - +
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Residues in contact with VAL1212 (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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1185A LEU* 3.8 13.4 - - + +
1193A ILE* 4.5 16.4 - - + -
1208A LEU* 2.7 49.3 + - + +
1209A LEU* 3.8 5.8 - - + +
1211A GLY* 1.3 72.0 - - - +
1213A SER* 1.3 64.5 + - - +
1215A ALA* 3.2 18.7 + - - +
1216A LYS* 3.4 10.7 + - - +
1224A ILE* 3.5 43.1 - - + -
1227A LEU* 4.5 15.5 - - + -
1228A LEU* 5.5 1.3 - - + -
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Residues in contact with SER1213 (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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1209A LEU 2.5 23.8 + - - -
1210A LEU 3.9 2.2 - - - -
1212A VAL* 1.3 77.5 - - - +
1214A ALA* 1.3 59.7 + - - +
1216A LYS* 3.1 5.6 + - - +
1217A LEU* 2.9 24.6 + - - -
1224A ILE* 4.4 0.7 - - - -
1228A LEU* 3.6 23.7 - - - +
1256A GLY* 3.7 18.9 - - - -
1259A LEU* 4.1 7.7 - - - +
1260A VAL* 3.8 24.8 - - - +
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Residues in contact with ALA1214 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1180A GLY 3.6 10.7 - - - +
1181A LEU* 3.5 30.6 - - + +
1210A LEU 2.9 21.6 + - - +
1211A GLY 3.7 0.9 - - - +
1213A SER* 1.3 72.3 - - - +
1215A ALA* 1.3 66.3 + - - +
1217A LEU* 3.2 22.3 - - - +
1259A LEU* 4.2 15.1 - - + +
1612A LEU* 4.6 12.4 - - + +
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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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1180A GLY* 3.3 11.1 + - - +
1183A GLY* 4.9 9.5 - - - +
1185A LEU 4.8 1.3 - - - -
1186A THR* 3.4 41.6 - - + +
1211A GLY 3.1 11.5 + - - +
1212A VAL* 3.2 13.5 - - - +
1213A SER 3.2 0.2 - - - -
1214A ALA* 1.3 79.4 - - - +
1216A LYS* 1.3 63.7 + - + +
1217A LEU* 3.3 4.0 + - - +
1219A THR* 5.2 0.2 + - - -
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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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1186A THR* 3.9 25.1 - - + +
1212A VAL 3.4 11.8 + - - +
1213A SER 3.1 7.6 + - - +
1215A ALA* 1.3 80.3 - - + +
1217A LEU* 1.3 62.8 - - - +
1218A GLY 3.3 1.1 - - - -
1219A THR* 2.5 41.2 + - + +
1221A ASP* 2.7 52.7 + - + +
1223A SER* 5.6 0.2 - - - -
1224A ILE* 3.7 21.5 - - + +
1260A VAL* 4.5 13.7 - - + -
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Residues in contact with LEU1217 (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 SER 2.9 11.9 + - - -
1214A ALA* 3.2 19.1 - - - +
1215A ALA 4.0 4.0 - - - +
1216A LYS* 1.3 76.9 - - - +
1218A GLY* 1.3 59.7 + - - +
1219A THR* 3.4 2.4 + - - -
1259A LEU* 3.5 10.3 - - + +
1262A GLN* 2.8 29.8 - - - +
1579A SER* 4.4 8.1 - - - +
1612A LEU* 3.9 31.6 - - + +
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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