Contacts of the helix formed by residues 1238 - 1249 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1109C LEU* 3.7 43.5 - - + -
1112C MET* 4.7 11.4 - - + -
1206C ALA* 5.1 1.8 - - + -
1236C ASN 3.4 6.9 - - - +
1237C CYS* 1.3 101.2 - - - +
1239C ASP* 1.3 66.2 + - - +
1240C MET* 3.0 5.3 + - - +
1241C LEU* 3.1 25.0 + - + +
1242C PHE* 3.5 1.0 + - - +
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Residues in contact with ASP1239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233C LYS* 2.7 36.2 + - - +
1237C CYS 3.8 2.5 - - - +
1238C PRO* 1.3 71.2 - - - +
1240C MET* 1.3 61.1 + - - +
1242C PHE* 3.6 3.7 + - - +
1243C GLU* 3.2 30.8 + - + +
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Residues in contact with MET1240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981B PHE* 3.4 51.2 - - + -
1109C LEU* 3.7 27.1 - - + -
1113C ILE* 3.4 37.7 - - + -
1238C PRO* 3.0 2.3 + - + +
1239C ASP* 1.3 79.1 - - - +
1241C LEU* 1.3 71.4 + - - +
1243C GLU* 3.5 3.4 + - - +
1244C LEU* 3.3 27.1 + - - +
1266C ILE* 5.1 4.5 - - + -
1269C GLU* 6.1 3.6 - - + -
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Residues in contact with LEU1241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109C LEU* 4.1 11.2 - - + -
1112C MET* 3.6 42.8 - - + +
1113C ILE* 3.9 20.9 - - + -
1116C ALA* 5.2 1.6 - - + -
1202C LEU* 4.0 30.2 - - + +
1205C ILE* 5.6 1.3 - - + -
1206C ALA* 4.9 5.8 - - + -
1237C CYS* 4.0 9.6 - - - -
1238C PRO* 3.1 24.8 + - + +
1240C MET* 1.3 77.9 - - - +
1242C PHE* 1.3 66.4 + - - +
1244C LEU* 3.2 12.4 + - + +
1245C MET* 3.1 30.9 + - + +
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Residues in contact with PHE1242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1231C LEU 4.0 15.0 - - - -
1232C ASP* 4.1 0.9 - - - -
1233C LYS* 3.6 66.4 - - + -
1234C PRO* 4.5 0.4 - - + -
1237C CYS* 3.9 8.2 - - - -
1238C PRO 3.5 3.6 + - - -
1239C ASP 4.0 6.7 - - - +
1240C MET 3.3 0.4 - - - -
1241C LEU* 1.3 78.7 - - - +
1243C GLU* 1.3 69.7 + - - +
1245C MET* 3.1 21.3 + - + +
1246C ARG* 2.9 50.3 + - + +
1249C TRP* 4.3 11.9 - + - -
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Residues in contact with GLU1243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981B PHE* 3.8 25.4 - - + +
982B SER* 5.1 2.8 - - - -
1041B MET* 4.5 4.3 - - - +
1239C ASP* 3.2 19.8 + - + +
1240C MET 3.9 4.7 - - - +
1241C LEU 3.3 0.6 - - - -
1242C PHE* 1.3 88.0 - - - +
1244C LEU* 1.3 63.1 + - - +
1246C ARG* 3.0 37.3 + - - +
1247C MET* 3.0 41.0 + - + +
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Residues in contact with LEU1244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981B PHE* 4.0 12.8 - - + -
986B VAL* 4.0 27.1 - - + -
1113C ILE* 5.9 0.9 - - + -
1116C ALA* 5.8 2.7 - - + -
1198C PHE* 5.6 0.7 - - + -
1202C LEU* 3.8 20.0 - - + -
1240C MET* 3.3 15.5 + - - +
1241C LEU* 3.2 20.7 + - + +
1242C PHE 3.2 0.6 - - - -
1243C GLU* 1.3 76.3 - - - +
1245C MET* 1.3 65.8 + - - +
1247C MET* 3.0 12.4 + - + +
1248C CYS* 2.9 27.8 + - - -
1257C PRO* 5.7 0.2 - - + -
1262C ILE* 4.7 28.3 - - + -
1265C SER* 4.3 4.5 - - - +
1266C ILE* 4.7 21.8 - - + -
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Residues in contact with MET1245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199C GLY* 3.8 12.6 - - - +
1202C LEU* 3.7 17.0 - - + +
1203C TRP* 3.6 39.3 - - - +
1206C ALA* 4.2 5.6 - - + -
1234C PRO* 4.5 2.5 - - + -
1237C CYS* 4.0 24.2 - - - -
1241C LEU* 3.1 21.4 + - + +
1242C PHE* 3.1 18.6 + - + +
1244C LEU* 1.3 75.3 - - - +
1246C ARG* 1.3 56.6 - - - +
1248C CYS* 3.2 7.7 + - - +
1249C TRP* 2.9 70.3 + - + -
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Residues in contact with ARG1246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040B SER* 6.1 0.2 - - - -
1041B MET* 3.3 51.0 - - + +
1230C LEU* 5.7 9.5 - - + +
1242C PHE* 2.9 46.5 + - + +
1243C GLU* 3.0 37.7 + - - +
1244C LEU 3.1 0.4 - - - -
1245C MET* 1.3 77.3 - - - +
1247C MET* 1.3 61.6 + - - +
1249C TRP* 3.3 17.6 + - + +
1250C GLN* 3.3 19.2 + - - +
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Residues in contact with MET1247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981B PHE* 3.8 16.8 - - + -
982B SER* 3.6 30.1 - - - +
983B ALA* 3.9 4.3 - - - +
986B VAL* 3.8 18.4 - - + -
987B TYR* 3.3 37.2 - - + +
1041B MET* 3.8 17.0 - - - -
1243C GLU* 3.0 31.4 - - + +
1244C LEU* 3.0 11.8 + - + +
1246C ARG* 1.3 75.9 - - - +
1248C CYS* 1.3 63.9 + - - +
1249C TRP 3.3 0.5 + - - -
1250C GLN* 3.4 20.7 - - - +
1256C ARG* 3.4 3.6 - - - +
1257C PRO* 3.3 20.1 - - + +
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Residues in contact with CYS1248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195C VAL* 3.6 40.6 - - - +
1196C TRP* 3.5 12.6 - - - -
1198C PHE* 4.0 11.9 - - - -
1199C GLY* 3.8 15.0 - - - -
1202C LEU* 5.2 1.3 - - - -
1244C LEU* 2.9 20.8 + - - -
1245C MET 3.5 8.3 - - - +
1247C MET* 1.3 77.1 - - - +
1249C TRP* 1.3 59.0 + - + +
1250C GLN 3.4 0.7 - - - -
1256C ARG* 3.2 22.3 + - - -
1257C PRO* 4.2 3.4 - - - -
1262C ILE* 4.0 20.0 - - - -
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Residues in contact with TRP1249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196C TRP* 3.2 56.3 + + + -
1199C GLY* 3.1 29.2 - - - -
1200C VAL* 3.6 8.1 - - + +
1203C TRP* 4.2 2.5 - + - -
1213C TYR* 5.8 0.9 - - - -
1230C LEU* 3.4 43.4 - - + +
1231C LEU* 3.8 53.8 - - + -
1242C PHE* 4.3 9.6 - + - -
1245C MET* 2.9 48.0 + - + +
1246C ARG* 3.3 10.9 + - + +
1247C MET 3.1 0.6 - - - -
1248C CYS* 1.3 84.5 - - + +
1250C GLN* 1.3 65.4 + - - +
1251C TYR* 3.3 2.6 + - - +
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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