Contacts of the helix formed by residues 1238 - 1249 (chain B) in PDB entry 2ZM3
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 PRO1238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106B PRO* 4.6 10.1 - - + -
1107B PRO 5.6 0.4 - - - +
1109B LEU* 3.7 51.6 - - + +
1112B MET* 4.9 10.8 - - - -
1206B ALA* 5.7 0.2 - - + -
1236B ASN 3.5 7.8 - - - +
1237B CYS* 1.3 92.0 - - - +
1239B ASP* 1.3 68.2 + - - +
1240B MET 4.4 2.5 - - - +
1241B LEU* 3.0 14.6 + - + +
1242B PHE* 3.4 7.3 + - - +
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Residues in contact with ASP1239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233B LYS* 2.9 30.2 + - - +
1237B CYS 3.8 3.1 - - - +
1238B PRO* 1.3 71.5 - - - +
1240B MET* 1.3 63.2 + - - +
1242B PHE* 3.2 4.2 + - - +
1243B GLU* 3.1 31.4 + - + +
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Residues in contact with MET1240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109B LEU* 4.4 21.3 - - + -
1113B ILE* 3.7 24.9 - - + -
1238B PRO* 3.1 0.9 + - + -
1239B ASP* 1.3 79.7 - - - +
1241B LEU* 1.3 70.7 + - - +
1243B GLU* 3.4 7.3 + - - +
1244B LEU* 3.3 29.8 + - + +
1265B SER* 5.2 3.8 - - - +
1266B ILE* 3.5 31.4 - - + -
1269B GLU* 6.3 1.6 - - + -
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Residues in contact with LEU1241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109B LEU* 4.4 12.3 - - + -
1112B MET* 3.4 43.3 - - + -
1113B ILE* 4.1 26.0 - - + +
1116B ALA* 5.4 1.3 - - + -
1202B LEU* 4.1 30.1 - - + +
1205B ILE* 6.3 0.2 - - + -
1206B ALA* 4.4 2.0 - - + -
1237B CYS* 4.1 4.5 - - - -
1238B PRO* 3.0 11.7 + - + +
1240B MET* 1.3 81.3 - - - +
1242B PHE* 1.3 66.1 + - - +
1244B LEU* 3.3 10.2 + - + +
1245B MET* 3.1 45.7 + - + +
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Residues in contact with PHE1242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230B LEU* 6.3 2.2 - - + -
1231B LEU 4.0 12.8 - - - -
1232B ASP* 3.8 6.3 - - - -
1233B LYS* 3.4 70.2 - - + +
1234B PRO* 4.3 2.2 - - + -
1237B CYS* 4.0 4.8 - - - -
1238B PRO 3.4 2.2 + - - -
1239B ASP 3.2 7.6 + - - +
1241B LEU* 1.3 75.9 - - - +
1243B GLU* 1.3 68.5 + - - +
1245B MET* 3.3 19.6 + - - +
1246B ARG* 2.9 54.3 + - + +
1249B TRP* 4.1 14.8 - + - -
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Residues in contact with GLU1243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233B LYS* 5.5 2.9 + - - -
1239B ASP* 3.1 19.0 + - + +
1240B MET* 3.7 8.7 - - - +
1241B LEU 3.3 0.2 - - - -
1242B PHE* 1.3 83.8 - - - +
1244B LEU* 1.3 61.0 + - - +
1246B ARG* 2.8 48.5 + - - +
1247B MET* 3.1 36.5 + - + +
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Residues in contact with LEU1244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113B ILE* 5.9 0.7 - - + -
1116B ALA* 5.6 1.3 - - + -
1198B PHE* 4.9 1.8 - - + -
1202B LEU* 3.9 22.2 - - + -
1240B MET* 3.3 29.2 + - + +
1241B LEU* 3.6 16.4 - - + +
1242B PHE 3.2 0.6 - - - -
1243B GLU* 1.3 77.6 - - - +
1245B MET* 1.3 64.7 + - - +
1247B MET* 3.2 31.2 + - + +
1248B CYS* 3.2 23.1 + - - -
1257B PRO* 5.3 1.6 - - + -
1262B ILE* 4.1 37.9 - - + -
1265B SER* 4.7 9.0 - - - +
1266B ILE* 4.8 10.1 - - + -
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Residues in contact with MET1245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199B GLY* 4.1 2.9 - - - +
1202B LEU* 3.9 17.5 - - + +
1203B TRP* 3.6 36.8 - - + +
1206B ALA* 4.1 4.3 - - + -
1234B PRO* 4.7 0.4 - - + -
1237B CYS* 4.0 19.1 - - - -
1241B LEU* 3.1 39.3 + - + +
1242B PHE* 3.3 19.7 - - + +
1244B LEU* 1.3 76.8 - - - +
1246B ARG* 1.3 55.8 + - - +
1248B CYS* 3.1 8.3 + - - +
1249B TRP* 2.9 70.2 + - + -
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Residues in contact with ARG1246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230B LEU* 5.5 12.3 - - + +
1242B PHE* 2.9 47.7 + - + +
1243B GLU* 2.8 40.7 + - - +
1244B LEU 3.2 0.2 - - - -
1245B MET* 1.3 77.7 - - - +
1247B MET* 1.3 60.3 + - + +
1249B TRP* 3.6 10.7 + - + +
1250B GLN* 3.0 33.8 + - - +
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Residues in contact with MET1247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243B GLU* 3.1 34.8 - - + +
1244B LEU* 3.6 22.4 - - + +
1245B MET 3.1 0.8 - - - -
1246B ARG* 1.3 75.7 - - + +
1248B CYS* 1.3 64.4 + - - +
1249B TRP 3.2 0.4 - - - -
1250B GLN* 3.2 26.4 + - + +
1255B MET 5.8 0.7 - - - +
1256B ARG* 3.5 2.8 - - - +
1257B PRO* 3.2 32.6 - - + +
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Residues in contact with CYS1248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195B VAL* 3.4 35.2 - - - +
1196B TRP* 3.7 10.7 - - - -
1198B PHE* 4.0 20.4 - - - -
1199B GLY* 3.9 15.5 - - - -
1202B LEU* 4.9 0.9 - - - -
1244B LEU* 3.2 22.2 + - - -
1245B MET 3.1 7.7 + - - +
1247B MET* 1.3 78.3 - - - +
1249B TRP* 1.3 58.2 + - + +
1250B GLN 3.2 0.4 - - - -
1256B ARG* 3.1 23.9 + - - -
1257B PRO* 4.1 9.2 - - - -
1262B ILE* 4.2 9.9 - - - -
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Residues in contact with TRP1249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196B TRP* 3.3 57.0 + + + -
1199B GLY* 3.3 30.2 - - - -
1200B VAL* 3.4 13.4 - - + +
1203B TRP* 4.0 5.4 - + + -
1213B TYR* 5.8 1.8 - - - -
1230B LEU* 3.6 42.7 - - + +
1231B LEU* 3.8 44.9 - - + -
1242B PHE* 4.1 11.0 - + - -
1245B MET* 2.9 49.2 + - + +
1246B ARG* 3.6 12.3 + - + +
1247B MET 3.2 0.6 - - - -
1248B CYS* 1.3 79.7 - - + +
1250B GLN* 1.3 64.7 + - - -
1251B TYR* 3.3 2.8 + - - +
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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