Contacts of the helix formed by residues 1238 - 1249 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1107D PRO 5.9 0.7 - - - +
1109D LEU* 3.7 52.0 - - + +
1112D MET* 5.0 12.6 - - + -
1206D ALA* 5.8 0.2 - - + -
1236D ASN 3.6 7.3 - - - +
1237D CYS* 1.3 100.4 - - - +
1239D ASP* 1.3 67.4 + - - +
1240D MET 3.0 3.7 + - - +
1241D LEU* 3.2 12.0 + - + -
1242D PHE* 3.5 1.6 + - - +
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Residues in contact with ASP1239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233D LYS* 2.8 29.0 + - - +
1237D CYS 4.0 2.6 - - - +
1238D PRO* 1.3 71.8 - - - +
1240D MET* 1.3 63.2 + - - +
1242D PHE* 3.4 2.6 + - - +
1243D GLU* 3.1 32.6 + - + +
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Residues in contact with MET1240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109D LEU* 4.3 24.2 - - + -
1113D ILE* 3.6 26.5 - - + -
1238D PRO* 3.0 1.2 - - + +
1239D ASP* 1.3 79.1 - - - +
1241D LEU* 1.3 70.0 + - - +
1243D GLU* 3.3 8.0 + - - +
1244D LEU* 3.3 31.4 + - + +
1265D SER* 5.3 2.9 - - - +
1266D ILE* 3.6 31.2 - - + -
1269D GLU* 5.2 8.3 - - - +
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Residues in contact with LEU1241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109D LEU* 4.3 13.5 - - + -
1112D MET* 3.4 46.9 - - + +
1113D ILE* 3.9 27.8 - - + -
1116D ALA* 5.2 1.3 - - + -
1202D LEU* 3.9 27.3 - - + +
1205D ILE* 5.5 0.4 - - + -
1206D ALA* 4.1 2.7 - - + -
1237D CYS* 4.1 6.1 - - - -
1238D PRO* 3.2 10.8 + - + +
1240D MET* 1.3 83.4 - - - +
1242D PHE* 1.3 58.5 + - - +
1244D LEU* 3.3 11.5 + - + +
1245D MET* 3.1 49.7 + - + +
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Residues in contact with PHE1242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230D LEU* 6.4 1.8 - - + -
1231D LEU 4.1 14.4 - - - -
1232D ASP* 4.1 1.3 - - - -
1233D LYS* 3.6 67.8 - - + -
1234D PRO* 4.4 0.9 - - + -
1237D CYS* 4.0 9.1 - - - -
1238D PRO 3.5 1.8 + - - -
1239D ASP 3.4 6.6 + - - +
1240D MET 3.2 0.6 - - - -
1241D LEU* 1.3 75.6 - - - +
1243D GLU* 1.3 69.1 + - - +
1244D LEU 3.1 2.0 - - - -
1245D MET* 3.1 21.9 + - - +
1246D ARG* 3.0 55.4 + - + +
1249D TRP* 4.4 12.3 - + - -
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Residues in contact with GLU1243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233D LYS* 5.9 0.3 + - - -
1239D ASP* 3.1 26.6 + - + +
1240D MET* 3.3 6.9 + - - +
1242D PHE* 1.3 84.8 - - - +
1244D LEU* 1.3 60.3 + - - +
1246D ARG* 2.9 42.9 + - - +
1247D MET* 3.1 40.4 + - + +
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Residues in contact with LEU1244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113D ILE* 5.7 0.7 - - + -
1116D ALA* 5.5 2.2 - - + -
1198D PHE* 4.9 1.1 - - + -
1202D LEU* 3.8 23.3 - - + -
1240D MET* 3.3 30.4 + - + +
1241D LEU* 3.3 17.0 - - + +
1242D PHE 3.1 0.8 - - - -
1243D GLU* 1.3 75.8 - - - +
1245D MET* 1.3 64.6 + - - +
1247D MET* 3.2 24.3 + - + +
1248D CYS* 3.1 26.8 + - - -
1257D PRO* 5.1 0.2 - - + -
1262D ILE* 3.9 41.7 - - + -
1265D SER* 4.9 7.9 - - - +
1266D ILE* 4.8 10.1 - - + -
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Residues in contact with MET1245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199D GLY* 3.8 11.9 - - - +
1202D LEU* 3.5 18.6 - - + +
1203D TRP* 3.5 48.7 - - + +
1206D ALA* 4.0 9.9 - - + -
1234D PRO* 4.9 0.4 - - + -
1237D CYS* 4.2 9.4 - - - -
1241D LEU* 3.1 32.3 + - + +
1242D PHE* 3.1 18.8 + - + +
1244D LEU* 1.3 77.6 - - - +
1246D ARG* 1.3 56.2 + - - +
1248D CYS* 3.2 7.3 + - - +
1249D TRP* 2.9 59.4 + - + -
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Residues in contact with ARG1246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230D LEU* 5.6 12.0 - - + +
1242D PHE* 3.0 48.2 + - + +
1243D GLU* 2.9 41.8 + - - +
1244D LEU 3.2 0.2 - - - -
1245D MET* 1.3 78.1 - - - +
1247D MET* 1.3 59.6 + - + +
1249D TRP* 3.3 17.3 + - + +
1250D GLN* 2.9 25.3 + - - +
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Residues in contact with MET1247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243D GLU* 3.1 31.6 - - + +
1244D LEU* 3.2 21.9 + - + +
1246D ARG* 1.3 76.9 - - + +
1248D CYS* 1.3 62.7 + - - +
1249D TRP 3.2 0.7 + - - -
1250D GLN* 3.3 26.2 + - - +
1255D MET 5.7 0.9 - - - +
1256D ARG* 3.5 2.8 - - - +
1257D PRO* 3.4 31.1 - - + +
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Residues in contact with CYS1248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195D VAL* 3.4 41.3 - - - +
1196D TRP* 3.5 13.5 - - - -
1198D PHE* 3.9 20.6 - - - -
1199D GLY* 3.8 15.3 - - - -
1202D LEU* 4.7 0.7 - - - -
1244D LEU* 3.1 21.1 + - - -
1245D MET 3.6 7.9 - - - +
1247D MET* 1.3 76.4 - - - +
1249D TRP* 1.3 59.0 + - + +
1250D GLN 3.4 0.9 - - - -
1256D ARG* 3.2 22.1 + - - -
1257D PRO* 4.1 1.3 - - - -
1262D ILE* 4.0 14.4 - - - -
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Residues in contact with TRP1249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196D TRP* 3.3 55.1 + + + -
1199D GLY* 3.3 27.0 - - - -
1200D VAL* 3.8 8.4 - - + +
1203D TRP* 4.1 2.2 - + + -
1213D TYR* 5.8 0.7 - - - -
1230D LEU* 3.5 41.6 - - + +
1231D LEU* 3.5 53.4 - - + -
1242D PHE* 4.4 9.4 - + - -
1245D MET* 2.9 49.8 + - + +
1246D ARG* 3.3 11.8 + - + +
1247D MET 3.1 0.8 - - - -
1248D CYS* 1.3 85.6 - - + +
1250D GLN* 1.3 65.0 + - - +
1251D TYR* 3.2 3.5 + - - +
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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