Contacts of the helix formed by residues 1212 - 1223 (chain A) in PDB entry 3F2B
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 CYS1212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1179A VAL* 6.3 0.4 - - + -
1180A GLN* 5.8 0.4 - - - -
1210A ILE* 4.1 1.7 - - - +
1211A GLY* 1.3 78.3 - - - +
1213A ARG* 1.3 67.2 + - - +
1214A ASP* 3.2 11.6 + - - -
1215A ASP* 3.3 50.2 + - - +
1216A ILE 3.9 1.7 + - - -
1270A MET* 3.4 17.5 - - - +
1271A PHE* 3.7 8.3 - - + +
1272A PRO 4.5 0.2 - - - -
1273A LYS* 3.8 41.7 - - + +
1276A ALA* 5.8 2.0 - - + -
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Residues in contact with ARG1213 (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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895A SER* 4.7 2.2 - - - -
962A THR* 3.9 20.1 + - + +
1212A CYS* 1.3 71.2 - - - +
1214A ASP* 1.3 73.6 + - - +
1216A ILE* 3.1 13.1 + - - +
1234A MET* 3.0 34.4 - - + +
1235A GLU* 4.0 8.2 + - - -
1238A ARG* 3.3 61.3 - - + +
1269A TYR* 4.2 10.7 + - - -
1270A MET* 2.9 36.5 + - + +
1271A PHE* 3.0 14.4 + - - +
1272A PRO* 3.4 22.8 - - + +
1456A DGT 3.3 32.1 + - - -
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Residues in contact with ASP1214 (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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898A SER* 4.5 0.5 + - - -
958A ILE* 3.4 20.7 - - - +
959A PRO* 4.0 15.9 - - + +
962A THR* 2.8 32.3 + - - +
1212A CYS* 3.1 7.1 - - - -
1213A ARG* 1.3 75.2 - - - +
1215A ASP* 1.3 64.7 + - - +
1217A MET* 2.9 6.2 + - - +
1218A VAL* 2.9 26.8 + - + +
1234A MET* 3.9 8.3 - - - -
1272A PRO* 3.4 6.1 - - - +
1273A LYS* 2.7 39.6 + - + +
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Residues in contact with ASP1215 (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 GLN* 4.5 11.6 + - - -
1207A SER 5.5 2.4 - - - +
1209A VAL 5.1 2.6 - - - +
1210A ILE* 5.6 5.4 - - + -
1211A GLY 4.7 5.0 + - - +
1212A CYS* 3.3 32.8 + - - +
1214A ASP* 1.3 78.5 - - - +
1216A ILE* 1.3 62.5 + - + +
1218A VAL* 4.1 10.0 - - - +
1219A TYR* 3.0 27.7 + - - +
1260A TYR* 4.4 1.3 - - - -
1273A LYS* 4.4 10.9 + - - -
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Residues in contact with ILE1216 (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 ILE* 3.9 19.3 - - + -
1213A ARG* 3.1 13.9 + - + +
1214A ASP 3.1 1.2 - - - -
1215A ASP* 1.3 77.4 - - - +
1217A MET* 1.3 64.4 + - - +
1219A TYR* 3.8 0.7 - - - +
1220A LEU* 3.1 42.2 + - + +
1233A ILE* 4.3 5.6 - - + -
1234A MET* 4.1 20.4 - - + +
1237A VAL* 3.4 37.2 - - + -
1260A TYR* 3.2 21.1 - - - +
1264A CYS* 4.5 11.2 - - - -
1270A MET* 3.7 15.5 - - + -
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Residues in contact with MET1217 (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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959A PRO* 5.1 9.4 - - - -
961A GLU* 3.9 13.2 - - + +
962A THR* 4.7 6.5 - - - -
966A PHE* 2.6 43.3 - - + -
1213A ARG 3.6 0.8 + - - -
1214A ASP* 2.9 8.3 + - - +
1216A ILE* 1.3 78.9 - - - +
1218A VAL* 1.3 66.7 + - + +
1220A LEU* 3.1 3.1 + - - -
1221A ILE* 3.0 33.4 + - + +
1227A PRO 3.7 0.9 - - - +
1230A ALA* 3.7 15.4 - - - +
1231A PHE* 2.8 40.4 - - + +
1234A MET* 3.7 25.6 - - - +
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Residues in contact with VAL1218 (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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957A ASP 6.1 0.2 - - - +
959A PRO* 4.1 28.3 - - + -
1214A ASP* 2.9 24.0 + - + +
1215A ASP* 4.1 10.5 - - - +
1217A MET* 1.3 78.8 - - + +
1219A TYR* 1.3 57.6 + - - +
1221A ILE* 3.6 9.5 + - + +
1222A TYR* 3.2 25.1 + - + +
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Residues in contact with TYR1219 (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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1215A ASP 3.0 19.2 + - - +
1216A ILE 3.8 1.6 - - - +
1218A VAL* 1.3 76.5 - - - +
1220A LEU* 1.3 69.1 + - + +
1222A TYR* 3.4 14.4 + + - +
1223A ARG* 2.8 64.7 + - + +
1256A VAL* 4.1 11.2 - - + -
1257A PRO* 3.3 27.5 - - - +
1259A TRP* 5.9 1.1 - + - -
1260A TYR* 3.5 49.0 - + + +
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Residues in contact with LEU1220 (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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1216A ILE* 3.1 30.0 + - + +
1219A TYR* 1.3 89.7 - - + +
1221A ILE* 1.3 60.9 + - - +
1223A ARG* 3.3 3.3 + - - -
1224A GLY 3.2 5.2 + - - -
1225A LEU* 3.0 38.9 + - + +
1230A ALA* 3.7 17.7 - - + +
1233A ILE* 3.6 45.1 - - + -
1251A MET* 4.2 19.3 - - + -
1256A VAL* 3.6 30.5 - - + -
1260A TYR* 4.8 0.7 - - + -
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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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966A PHE* 4.3 8.1 - - + -
1217A MET* 3.0 32.5 + - + +
1218A VAL* 3.8 8.3 - - + +
1220A LEU* 1.3 75.6 - - - +
1222A TYR* 1.3 66.3 + - - +
1224A GLY* 2.8 17.0 + - - -
1225A LEU 3.8 8.4 - - - +
1227A PRO* 3.8 38.6 - - + -
1230A ALA* 3.8 12.1 - - + -
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Residues in contact with TYR1222 (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 VAL* 3.2 13.9 + - + +
1219A TYR* 3.4 22.7 - + - +
1221A ILE* 1.3 80.3 - - - +
1223A ARG* 1.3 83.0 + - - +
1224A GLY* 2.9 6.8 + - - -
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Residues in contact with ARG1223 (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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1219A TYR* 2.8 58.9 + - + +
1220A LEU* 3.6 8.1 - - - +
1221A ILE 3.2 0.4 - - - -
1222A TYR* 1.3 90.6 - - - +
1224A GLY* 1.3 56.2 + - - +
1225A LEU* 3.7 2.5 - - + -
1254A HIS* 3.2 45.9 + - - +
1255A ASP* 3.4 26.7 + - - +
1256A VAL* 4.1 14.4 - - + -
1257A PRO* 5.1 4.2 - - - +
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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