Contacts of the helix formed by residues 1216 - 1234 (chain A) in PDB entry 3B13
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 ARG1216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1210A PHE* 3.5 28.5 - - - -
1211A TYR* 3.0 34.6 + - + +
1214A ASN* 3.6 30.3 - - + +
1215A ASN* 1.3 75.8 - - - +
1217A GLU* 1.3 64.9 + - - +
1218A GLU* 3.4 2.2 - - + -
1219A MET* 3.5 12.6 + - + +
1220A TYR* 3.1 22.5 + - - +
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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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1215A ASN 3.8 4.6 + - - +
1216A ARG* 1.3 70.9 - - - +
1218A GLU* 1.3 66.8 + - - +
1220A TYR* 3.3 6.7 + - + +
1221A ILE* 2.9 38.3 + - + +
1250A LEU* 4.1 21.0 - - + +
1261A GLN* 3.3 26.7 + - + +
1262A VAL* 3.1 38.9 - - - +
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Residues in contact with GLU1218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216A ARG* 3.4 1.1 - - + -
1217A GLU* 1.3 80.0 - - - +
1219A MET* 1.3 70.4 + - + +
1221A ILE* 3.3 4.4 + - - +
1222A ARG* 3.0 27.2 + - - +
1260A SER* 4.6 6.2 + - - +
1261A GLN* 3.7 41.5 + - + +
1263A MET 5.6 2.5 - - - +
1265A THR* 5.5 10.8 - - + -
1268A GLN* 5.9 1.0 + - - -
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Residues in contact with MET1219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211A TYR* 3.4 44.9 - - + -
1216A ARG* 3.5 16.4 + - + +
1217A GLU 3.3 0.6 - - - -
1218A GLU* 1.3 91.6 - - + +
1220A TYR* 1.3 64.8 + - - +
1222A ARG* 3.2 55.7 + - + +
1223A TYR* 3.0 33.0 + - - -
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Residues in contact with TYR1220 (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 LEU* 3.0 48.4 - - + +
1209A ASN* 5.9 0.2 - - - -
1211A TYR* 3.6 13.8 - - + +
1212A LYS* 3.5 40.6 - - + +
1216A ARG 3.1 18.6 + - - +
1217A GLU* 3.6 7.9 - - + +
1219A MET* 1.3 77.6 - - - +
1221A ILE* 1.3 69.3 + - + +
1224A LEU* 3.0 42.0 + - + +
1246A LEU* 3.6 34.6 + - - +
1250A LEU* 4.3 24.7 - - + -
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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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1217A GLU* 2.9 39.3 + - + +
1218A GLU 3.6 4.7 - - - +
1220A TYR* 1.3 73.9 - - + +
1222A ARG* 1.3 69.8 + - - +
1224A LEU* 2.9 33.4 + - + +
1225A TYR* 3.1 26.2 + - + -
1247A HIS* 4.0 17.9 - - + -
1250A LEU* 4.0 15.3 - - + -
1261A GLN 3.7 17.0 - - - +
1262A VAL* 4.1 16.2 - - + +
1263A MET 4.6 3.1 - - - +
1264A GLN* 4.3 21.1 - - - +
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Residues in contact with ARG1222 (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 GLU 3.0 14.8 + - - +
1219A MET* 3.2 39.5 + - + +
1221A ILE* 1.3 79.2 - - - +
1223A TYR* 1.3 76.0 + - + +
1225A TYR* 3.1 10.0 + - - +
1226A LYS* 3.0 33.0 + - + +
1264A GLN* 6.3 1.6 - - - -
1265A THR* 4.5 26.1 + - + +
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Residues in contact with TYR1223 (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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1204A THR* 3.7 32.3 - - + +
1207A LEU* 3.4 42.0 - - + +
1208A LEU* 3.7 23.8 - - + -
1211A TYR* 3.9 20.9 + + + -
1219A MET* 3.0 25.7 + - - +
1222A ARG* 1.3 89.2 - - + +
1224A LEU* 1.3 67.8 + - - +
1226A LYS* 3.0 31.0 + - + +
1227A LEU* 2.9 24.6 + - - +
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Residues in contact with LEU1224 (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 LEU* 3.6 17.1 - - + +
1220A TYR* 3.0 31.2 + - + +
1221A ILE* 2.9 19.8 + - + +
1223A TYR* 1.3 73.4 - - - +
1225A TYR* 1.3 65.0 + - + +
1227A LEU* 3.3 2.1 + - - +
1228A ARG* 2.9 23.7 + - - +
1243A THR* 3.4 23.4 - - + +
1244A LEU* 5.5 2.0 - - + -
1246A LEU* 3.5 36.6 - - + -
1247A HIS* 3.4 42.8 - - + +
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Residues in contact with TYR1225 (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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1221A ILE* 3.1 30.1 + - + -
1222A ARG* 3.1 7.6 + - - +
1224A LEU* 1.3 81.7 - - + +
1226A LYS* 1.3 63.5 + - - +
1228A ARG* 3.4 34.9 + - - +
1229A ASP* 3.0 32.0 + - - +
1244A LEU* 3.2 28.4 - - + +
1247A HIS* 2.6 39.6 + + + -
1264A GLN* 3.7 51.0 + - + +
1267A GLN* 4.7 2.9 + - - -
1280A LEU* 3.9 15.8 - - + +
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Residues in contact with LYS1226 (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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1200A ARG* 5.6 6.3 - - - +
1204A THR* 4.2 13.0 - - + -
1222A ARG* 3.0 22.4 + - + +
1223A TYR* 3.0 49.9 + - + +
1225A TYR* 1.3 75.1 - - - +
1227A LEU* 1.3 62.7 + - - +
1229A ASP* 2.9 19.1 + - - +
1230A LEU* 3.0 19.8 + - + +
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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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1201A MET* 4.2 23.1 - - + +
1204A THR* 3.9 12.8 - - + +
1205A VAL* 3.7 32.1 - - + -
1208A LEU* 4.6 10.5 - - + -
1223A TYR 2.9 11.3 + - - +
1224A LEU* 3.5 8.7 - - - +
1226A LYS* 1.3 75.8 - - - +
1228A ARG* 1.3 62.1 + - - +
1230A LEU* 3.3 7.2 + - + +
1231A HIS* 3.0 51.4 + - + +
1243A THR* 3.7 18.4 - - + +
1246A LEU* 5.9 0.4 - - + -
1478A ILE* 4.1 17.7 - - + +
1479A LEU* 4.7 0.7 - - + -
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Residues in contact with ARG1228 (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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1224A LEU 2.9 18.0 + - - +
1225A TYR* 3.7 35.0 + - - +
1226A LYS 3.2 0.2 - - - -
1227A LEU* 1.3 75.4 - - - +
1229A ASP* 1.3 83.4 + - - +
1231A HIS* 3.3 7.5 + - - +
1232A LEU* 2.9 32.6 + - + +
1240A ALA* 4.0 20.0 - - + +
1243A THR* 4.1 12.3 - - + +
1244A LEU* 3.8 21.8 - - + +
1264A GLN* 4.5 8.9 + - - +
1283A THR* 5.1 2.2 - - - +
1287A TYR* 3.5 30.8 + - + -
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Residues in contact with ASP1229 (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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1225A TYR* 3.0 19.4 + - - +
1226A LYS* 2.9 11.5 + - - +
1228A ARG* 1.3 105.1 + - - +
1230A LEU* 1.3 64.4 + - + +
1232A LEU* 3.4 7.8 + - - +
1233A ASP* 2.9 32.6 + - - +
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Residues in contact with LEU1230 (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 LYS* 3.9 17.2 + - + +
1200A ARG* 3.8 42.8 - - + +
1201A MET* 3.6 40.3 - - + +
1204A THR* 3.6 27.6 - - - +
1226A LYS* 3.0 19.9 + - + +
1227A LEU* 3.5 9.2 - - - +
1228A ARG 3.2 0.2 - - - -
1229A ASP* 1.3 75.9 - - + +
1231A HIS* 1.3 64.6 + - - +
1233A ASP* 2.9 25.7 + - - +
1234A CYS* 3.1 6.4 + - - -
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Residues in contact with HIS1231 (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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1201A MET* 3.8 25.0 - - - +
1227A LEU* 3.0 33.2 + - + +
1228A ARG 3.6 6.1 - - - +
1230A LEU* 1.3 74.4 - - - +
1232A LEU* 1.3 63.0 + - - +
1234A CYS* 2.9 9.2 + - - +
1236A ASN* 2.9 54.1 + - - +
1239A GLU* 3.5 20.6 - - + +
1240A ALA* 3.9 11.2 - - + -
1243A THR* 3.5 19.1 - - - -
1478A ILE 2.5 30.1 + - - -
1479A LEU* 4.4 6.3 - - + -
1480A ARG 5.1 0.7 - - - -
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Residues in contact with LEU1232 (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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1228A ARG* 2.9 34.2 + - + +
1229A ASP* 4.1 6.7 - - - +
1231A HIS* 1.3 72.7 - - - +
1233A ASP* 1.3 62.4 + - - +
1235A ASP* 3.1 21.0 + - - +
1236A ASN 4.5 1.3 - - - +
1237A TYR* 3.8 32.4 + - + -
1240A ALA* 3.6 24.5 - - + -
1287A TYR* 3.2 30.3 - - + +
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Residues in contact with ASP1233 (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 LYS* 3.2 29.3 + - - +
1229A ASP* 2.9 25.0 + - - +
1230A LEU* 2.9 17.0 + - - +
1232A LEU* 1.3 79.3 - - - +
1234A CYS* 1.3 57.5 + - - +
1235A ASP* 3.5 4.2 + - - +
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Residues in contact with CYS1234 (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 LYS* 4.6 22.4 - - - -
1201A MET* 4.0 23.6 - - - -
1230A LEU 3.1 5.4 + - - +
1231A HIS 2.9 7.3 + - - +
1233A ASP* 1.3 76.3 - - - +
1235A ASP* 1.3 70.6 + - - +
1236A ASN* 3.5 25.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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