Contacts of the helix formed by residues 1235 - 1246 (chain E) in PDB entry 5HZN
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 PRO1235 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106E LEU* 3.6 46.0 - - + -
1109E MET* 3.7 23.3 - - + -
1203E ALA* 5.5 0.9 - - + -
1233E ASN 3.4 9.2 - - - +
1234E CYS* 1.3 93.4 - - - +
1236E ASP* 1.3 64.4 + - - +
1237E MET* 4.4 4.5 - - + +
1238E LEU* 3.1 16.6 + - + -
1239E PHE* 3.3 8.8 + - - +
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Residues in contact with ASP1236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230E LYS* 2.7 34.9 + - - +
1234E CYS 3.9 2.4 - - - +
1235E PRO* 1.3 71.2 - - - +
1237E MET* 1.3 57.9 + - - +
1239E PHE* 3.5 3.3 + - - +
1240E GLU* 3.0 28.6 + - - +
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Residues in contact with MET1237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106E LEU* 4.4 11.2 - - + -
1110E ILE* 3.3 36.3 - - + -
1235E PRO* 3.1 5.2 + - + -
1236E ASP* 1.3 80.3 - - - +
1238E LEU* 1.3 77.6 + - - +
1240E GLU* 3.5 8.1 + - + +
1241E LEU* 3.2 24.5 + - + +
1244E MET* 5.4 0.5 - - - +
1262E SER 6.0 0.2 - - - +
1263E ILE* 4.5 20.9 - - + -
1266E GLU* 4.9 11.4 - - + -
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Residues in contact with LEU1238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106E LEU* 4.2 14.4 - - + -
1109E MET* 3.8 46.4 - - + -
1110E ILE* 4.9 7.9 - - + +
1113E ALA* 5.2 5.8 - - + -
1199E LEU* 4.2 27.3 - - + +
1202E ILE* 5.6 1.6 - - + -
1203E ALA* 4.5 12.1 - - + -
1234E CYS* 3.9 5.4 - - - -
1235E PRO* 3.1 18.4 + - + +
1237E MET* 1.3 87.8 - - - +
1239E PHE* 1.3 64.4 + - - +
1241E LEU* 3.2 12.6 + - + +
1242E MET* 3.0 30.5 + - + +
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Residues in contact with PHE1239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1227E LEU* 6.6 0.2 - - + -
1228E LEU 4.2 13.2 - - - -
1229E ASP* 4.3 0.7 - - - -
1230E LYS* 3.6 66.9 - - + -
1231E PRO* 4.6 0.2 - - + -
1234E CYS* 3.8 7.0 - - - -
1235E PRO 3.3 5.2 + - - +
1236E ASP 3.9 6.3 - - - +
1237E MET 3.4 0.2 - - - -
1238E LEU* 1.3 79.0 - - - +
1240E GLU* 1.3 61.7 + - - +
1242E MET* 3.2 21.6 + - + +
1243E ARG* 2.9 49.8 + - + +
1246E TRP* 4.4 12.1 - + - -
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Residues in contact with GLU1240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1236E ASP 3.0 17.9 + - - +
1237E MET* 3.5 9.9 - - - +
1238E LEU 3.2 0.2 - - - -
1239E PHE* 1.3 81.3 - - - +
1241E LEU* 1.3 61.3 - - - +
1243E ARG* 3.4 27.9 + - - +
1244E MET* 3.1 42.6 + - + +
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Residues in contact with LEU1241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113E ALA* 5.4 2.2 - - + -
1195E PHE* 4.7 1.6 - - + -
1199E LEU* 3.7 22.2 - - + -
1237E MET* 3.2 15.9 + - + +
1238E LEU* 3.2 19.6 + - + +
1240E GLU* 1.3 72.2 - - - +
1242E MET* 1.3 65.4 + - - +
1244E MET* 3.1 27.2 + - + +
1245E CYS* 3.0 28.3 + - - -
1259E ILE* 4.0 42.6 - - + -
1262E SER* 4.2 12.1 - - - +
1263E ILE* 4.3 20.9 - - + -
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Residues in contact with MET1242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196E GLY* 3.6 17.9 - - - +
1199E LEU* 3.8 32.5 - - + +
1200E TRP* 3.8 18.2 - - - +
1203E ALA* 4.1 4.0 - - + -
1231E PRO* 4.7 1.8 - - + -
1234E CYS* 3.8 26.0 - - - -
1238E LEU* 3.0 26.5 + - + +
1239E PHE* 3.2 20.8 + - + +
1241E LEU* 1.3 72.6 - - - +
1243E ARG* 1.3 58.2 + - - +
1245E CYS* 3.1 9.1 + - - +
1246E TRP* 2.9 67.1 + - + -
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Residues in contact with ARG1243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1227E LEU* 5.8 8.7 - - + -
1239E PHE* 2.9 33.2 + - + +
1240E GLU* 3.4 31.1 + - - +
1242E MET* 1.3 76.3 - - - +
1244E MET* 1.3 59.9 + - + +
1246E TRP* 3.5 17.6 + - - +
1247E GLN* 3.2 29.6 + - - +
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Residues in contact with MET1244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237E MET 5.4 0.2 - - - +
1240E GLU* 3.1 44.1 + - + +
1241E LEU* 3.1 30.3 + - + +
1243E ARG* 1.3 73.2 - - + +
1245E CYS* 1.3 66.0 + - - +
1246E TRP 3.3 0.7 + - - -
1247E GLN* 3.3 23.7 + - - +
1252E MET 5.9 0.2 - - - +
1253E ARG* 3.7 2.6 - - - -
1254E PRO* 3.3 36.9 - - + +
1262E SER* 5.8 3.6 - - - +
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Residues in contact with CYS1245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192E VAL* 3.4 41.3 - - - +
1193E TRP* 3.5 12.1 - - - -
1195E PHE* 3.9 23.1 - - - -
1196E GLY* 3.7 15.9 - - - -
1199E LEU* 5.1 0.7 - - - -
1241E LEU* 3.0 20.6 + - - -
1242E MET 3.4 8.1 - - - +
1244E MET* 1.3 76.1 - - - +
1246E TRP* 1.3 57.7 + - + +
1247E GLN 3.4 0.7 - - - -
1253E ARG* 3.1 23.0 + - - -
1254E PRO* 4.6 2.7 - - - -
1259E ILE* 4.0 9.6 - - - -
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Residues in contact with TRP1246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193E TRP* 3.4 54.3 + + + -
1196E GLY* 3.3 24.4 - - - -
1197E VAL* 3.5 14.7 - - + +
1200E TRP* 4.0 4.3 - + + -
1210E TYR* 5.7 1.6 - - - -
1227E LEU* 3.7 36.5 - - + +
1228E LEU* 3.7 57.9 - - + -
1239E PHE* 4.4 9.0 - + - -
1242E MET* 2.9 47.1 + - + +
1243E ARG* 3.5 11.9 + - - +
1244E MET 3.1 0.8 - - - -
1245E CYS* 1.3 82.9 - - + +
1247E GLN* 1.3 64.6 + - - +
1248E TYR* 3.3 2.4 + - - -
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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