Contacts of the helix formed by residues 1213 - 1218 (chain D) in PDB entry 3CMT
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 ASN1213 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195D ILE 4.2 16.4 - - - +
196D ARG* 4.3 3.1 - - - -
197D MET* 4.0 23.6 - - - +
1168D ALA 5.7 0.2 + - - -
1212D GLY* 1.3 73.9 - - - -
1214D ALA* 1.3 66.3 + - - +
1215D LEU 3.3 2.5 - - - -
1216D LYS* 2.9 45.0 + - - +
1217D PHE* 3.3 20.8 - - + -
1004E C 2.7 48.5 + - - +
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Residues in contact with ALA1214 (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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196D ARG* 3.5 25.4 - - - +
1168D ALA 5.1 0.7 - - - +
1171D MET* 4.2 4.9 - - + +
1172D SER* 3.5 38.1 - - - +
1175D MET* 3.8 12.8 - - + -
1212D GLY 3.7 0.8 - - - -
1213D ASN* 1.3 77.3 - - - +
1215D LEU* 1.3 63.5 + - - +
1217D PHE* 3.0 13.3 + - - +
1218D TYR* 3.2 19.7 + - + -
1004E C 4.2 1.0 + - - -
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Residues in contact with LEU1215 (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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1061D ILE* 3.7 29.8 - - + -
1063D GLU* 3.4 42.0 - - + +
1146D VAL* 4.3 13.7 - - + -
1171D MET* 5.6 8.2 - - + +
1175D MET* 3.9 19.0 - - + +
1191D PHE* 3.7 28.7 - - + -
1193D ASN* 4.5 2.5 - - - +
1209D THR* 5.5 3.4 - - + -
1210D THR 5.7 1.3 - - - +
1211D GLY 5.3 5.7 + - - +
1212D GLY 5.1 3.4 + - - +
1213D ASN 3.3 0.6 - - - -
1214D ALA* 1.3 76.2 - - - +
1216D LYS* 1.3 66.4 + - - +
1218D TYR 4.5 0.4 - - - +
1219D ALA* 2.9 32.1 + - + +
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Residues in contact with LYS1216 (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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68D GLU* 3.1 39.1 - - + +
1063D GLU* 4.6 0.6 + - - -
1208D THR* 4.3 21.6 - - - +
1209D THR* 4.8 12.9 + - + +
1212D GLY 4.2 10.0 + - - +
1213D ASN* 2.9 41.5 + - + +
1214D ALA 3.3 0.2 + - - -
1215D LEU* 1.3 78.6 - - - +
1217D PHE* 1.3 53.5 + - + +
1219D ALA 4.0 1.0 + - - -
1222D ARG* 4.1 35.2 - - - +
1248D LYS* 2.7 36.0 + - - +
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Residues in contact with PHE1217 (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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66D GLY 3.3 16.6 - - - -
67D PRO* 3.5 5.6 - - + -
68D GLU* 3.3 31.4 - - + -
72D LYS* 3.8 3.6 - - - -
96D GLU* 4.3 2.0 - - - +
194D GLN* 3.4 48.9 - - + +
195D ILE* 3.4 38.4 - - + -
196D ARG* 3.7 2.5 - - - -
501D ALF 3.1 32.9 - - - -
1213D ASN* 3.3 26.0 - - + -
1214D ALA 3.0 4.5 + - - +
1216D LYS* 1.3 81.5 - - + +
1218D TYR* 1.3 61.9 + - + +
1219D ALA 3.7 0.5 - - - +
1248D LYS* 2.8 16.6 + - - -
1250D LYS* 3.8 7.1 + - - -
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Residues in contact with TYR1218 (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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96D GLU* 4.7 15.2 - - + +
98D ALA* 5.7 1.7 - - - +
147D ALA* 3.2 25.6 + - - +
148D ALA* 3.3 22.6 - - + -
194D GLN* 3.8 25.1 - - - -
196D ARG* 4.0 9.5 + - - -
1061D ILE* 4.0 25.1 + - + +
1172D SER 5.1 1.8 - - - -
1175D MET* 3.4 46.4 - - + -
1176D ARG* 3.6 10.9 - - - +
1179D ALA* 4.0 22.4 - - + -
1214D ALA* 3.2 24.3 + - + +
1215D LEU* 3.3 1.1 + - - +
1217D PHE* 1.3 77.5 - - - +
1219D ALA* 1.3 65.3 + - - +
1220D SER* 3.4 8.0 + - - -
1250D LYS* 4.7 5.9 + - - +
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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