Contacts of the helix formed by residues 1217 - 1227 (chain A) 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 SER1217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1177A ARG* 3.5 3.6 - - - +
1216A LEU* 1.3 75.9 - - - +
1218A ASN* 1.3 66.1 + - - +
1219A GLU* 3.5 9.1 + - - +
1220A GLN* 2.8 45.0 + - - +
1221A VAL* 2.9 11.6 + - - +
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Residues in contact with ASN1218 (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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1176A VAL* 3.8 28.2 - - + +
1177A ARG* 3.0 31.2 + - - +
1211A GLN* 5.2 0.3 + - - -
1217A SER* 1.3 72.8 - - - +
1219A GLU* 1.3 60.2 + - - +
1221A VAL* 3.4 5.7 + - - +
1222A LEU* 3.2 19.8 + - - +
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Residues in contact with GLU1219 (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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1217A SER* 3.1 8.8 + - - +
1218A ASN* 1.3 79.6 - - - +
1220A GLN* 1.3 61.3 + - - +
1222A LEU* 3.5 16.7 + - + +
1223A ARG* 3.5 45.9 + - - +
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Residues in contact with GLN1220 (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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1215A GLY 4.2 3.6 - - - +
1216A LEU* 3.6 25.0 - - + +
1217A SER* 2.8 42.6 + - - +
1219A GLU* 1.3 75.3 - - - +
1221A VAL* 1.3 60.6 + - - +
1222A LEU 3.3 0.2 - - - -
1223A ARG* 3.5 24.6 + - - +
1224A PHE* 3.0 30.7 + - - +
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Residues in contact with VAL1221 (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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1176A VAL* 4.4 9.0 - - + +
1177A ARG* 3.7 49.8 - - + +
1184A LEU* 5.8 0.7 - - + -
1213A TYR* 3.7 33.4 - - + -
1216A LEU* 4.0 7.0 - - + -
1217A SER 2.9 19.0 + - - +
1218A ASN* 3.6 8.7 - - - +
1219A GLU 3.3 0.2 - - - -
1220A GLN* 1.3 75.3 - - - +
1222A LEU* 1.3 65.2 - - - +
1224A PHE* 4.2 4.9 - - - -
1225A VAL* 2.9 36.2 + - + +
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Residues in contact with LEU1222 (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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1176A VAL* 4.5 16.1 - - + +
1184A LEU* 3.5 46.3 - - + +
1218A ASN 3.2 9.6 + - - +
1219A GLU* 3.6 15.0 - - + +
1220A GLN 3.3 0.2 - - - -
1221A VAL* 1.3 80.4 - - - +
1223A ARG* 1.3 59.9 + - + +
1226A MET* 3.0 44.0 + - - +
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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 GLU* 3.5 46.3 + - - +
1220A GLN* 3.6 32.0 - - - +
1222A LEU* 1.3 76.8 - - + +
1224A PHE* 1.3 67.0 + - - +
1226A MET* 3.5 3.2 + - - -
1227A GLU* 3.2 44.8 + - - +
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Residues in contact with PHE1224 (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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1213A TYR* 3.8 30.5 - + - -
1216A LEU* 3.9 19.1 - - + -
1220A GLN 3.0 20.0 + - - +
1221A VAL* 3.7 3.1 - - - +
1223A ARG* 1.3 79.5 - - - +
1225A VAL* 1.3 62.2 + - + +
1227A GLU* 3.4 6.7 + - - +
1228A GLY 3.4 0.3 + - - -
1229A GLY* 2.9 31.3 + - - -
1230A LEU 3.4 40.4 - - - -
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Residues in contact with VAL1225 (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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1176A VAL 5.8 0.9 - - - +
1179A MET 4.0 7.6 - - - +
1181A PRO* 3.5 18.8 - - + +
1184A LEU* 3.6 22.4 - - + -
1196A TRP* 3.8 25.5 - - + -
1213A TYR* 3.3 42.0 - - + +
1221A VAL* 2.9 25.8 + - + +
1224A PHE* 1.3 76.2 - - + +
1226A MET* 1.3 63.9 + - - +
1227A GLU 3.2 2.2 + - - -
1228A GLY* 3.4 9.2 + - - -
1229A GLY 4.0 10.1 - - - +
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Residues in contact with MET1226 (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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1181A PRO* 3.8 24.3 - - - +
1184A LEU* 3.9 7.4 - - + +
1185A LYS* 3.9 38.9 - - + +
1222A LEU* 3.0 40.1 + - + +
1223A ARG* 4.0 4.7 - - - +
1224A PHE 3.3 0.2 - - - -
1225A VAL* 1.3 78.6 - - - +
1227A GLU* 1.3 60.2 + - + +
1228A GLY 3.4 0.4 - - - -
1251A TYR* 2.8 29.3 + - - -
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Residues in contact with GLU1227 (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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1223A ARG* 3.2 33.9 + - - +
1224A PHE* 3.4 2.6 + - - +
1225A VAL 3.2 0.4 - - - -
1226A MET* 1.3 82.9 - - + +
1228A GLY* 1.3 56.0 + - - +
1229A GLY 3.6 2.4 + - - -
1251A TYR* 4.4 4.7 - - - -
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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