Contacts of the helix formed by residues 1202 - 1213 (chain A) in PDB entry 6CNB
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 ILE1202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1188A ILE* 5.7 2.2 - - + -
1201A THR* 1.3 86.7 - - + +
1203A GLU* 1.3 68.5 + - + +
1204A ASP 2.7 4.7 + - - -
1205A ILE* 2.5 58.3 + - + +
1206A ALA* 2.8 13.8 + - + -
1224A ILE* 3.5 45.3 - - + +
1228A ASP* 4.0 11.0 - - - +
1229A ARG 3.1 35.2 - - - +
1230A ILE* 4.8 4.0 - - + -
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Residues in contact with GLU1203 (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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1201A THR* 5.0 0.8 - - - -
1202A ILE* 1.3 83.7 - - + +
1204A ASP* 1.3 62.8 + - - +
1206A ALA* 3.5 18.7 - - - +
1207A VAL* 2.9 34.6 + - + +
1222A VAL* 5.0 8.9 - - - +
1223A ASN* 5.9 1.9 - - - -
1224A ILE* 5.6 4.5 - - - +
1E MET* 5.2 10.3 - - + -
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Residues in contact with ASP1204 (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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1199A GLU 3.8 7.0 - - - +
1200A LEU* 3.3 35.3 + - + -
1201A THR* 3.8 4.7 + - - +
1202A ILE 2.7 4.3 + - - +
1203A GLU* 1.3 75.8 - - - +
1205A ILE* 1.3 57.8 + - + +
1207A VAL* 3.1 9.5 - - - +
1208A ALA* 2.9 27.6 + - - +
1E MET* 3.4 32.3 - - - +
3E GLN* 4.7 8.1 - - - +
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Residues in contact with ILE1205 (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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1169A VAL* 5.9 1.6 - - + -
1188A ILE* 4.0 26.9 - - + -
1200A LEU* 3.8 31.0 - - + -
1201A THR 5.3 0.4 - - - +
1202A ILE* 2.5 42.8 + - + +
1204A ASP* 1.3 72.8 - - + +
1206A ALA* 1.3 65.7 + - - +
1208A ALA* 3.3 9.3 - - - +
1209A ILE* 2.9 38.1 + - + +
1230A ILE* 4.7 13.2 - - + -
1272A VAL* 3.5 29.4 - - + +
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Residues in contact with ALA1206 (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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1202A ILE* 2.8 15.2 + - + +
1203A GLU* 3.4 33.7 - - - +
1204A ASP 3.2 0.2 - - - -
1205A ILE* 1.3 85.5 - - - +
1207A VAL* 1.3 64.6 + - - +
1209A ILE* 3.1 19.0 + - - +
1210A THR* 3.7 2.9 + - - +
1222A VAL* 4.1 32.8 - - + +
1223A ASN* 6.4 1.1 - - - -
1230A ILE* 6.1 2.0 - - + -
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Residues in contact with VAL1207 (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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1203A GLU* 2.9 28.3 + - + +
1204A ASP* 3.1 19.1 - - - +
1206A ALA* 1.3 73.8 - - - +
1208A ALA* 1.3 61.6 + - - +
1210A THR* 3.0 19.2 - - + +
1211A ARG* 2.9 59.4 + - + +
1222A VAL* 5.1 1.5 - - - +
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Residues in contact with ALA1208 (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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1204A ASP 2.9 19.8 + - - +
1205A ILE* 3.3 13.0 - - + +
1206A ALA 3.1 0.2 - - - -
1207A VAL* 1.3 77.4 - - + +
1209A ILE* 1.3 64.5 + - + +
1211A ARG* 3.1 11.6 + - - +
1212A ALA* 2.9 26.0 + - - +
1271A VAL 4.7 2.8 - - - +
1272A VAL* 4.0 25.6 - - - +
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Residues in contact with ILE1209 (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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1166A LEU* 4.0 26.2 - - + -
1205A ILE* 2.9 33.8 + - + +
1206A ALA* 3.1 11.0 + - - +
1208A ALA* 1.3 78.1 - - + +
1210A THR* 1.3 54.7 + - - +
1212A ALA* 3.1 3.8 + - - +
1213A SER* 2.6 40.3 + - - -
1217A ILE* 5.8 5.4 - - + -
1222A VAL* 6.2 4.5 - - + -
1230A ILE* 5.8 5.8 - - + -
1232A ILE* 5.5 11.2 - - + -
1267A LEU* 4.4 24.2 - - + -
1270A VAL* 4.7 8.0 - - + +
1271A VAL 5.3 3.4 - - - +
1272A VAL* 6.1 2.0 - - + -
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Residues in contact with THR1210 (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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1206A ALA 3.7 1.9 + - - +
1207A VAL* 3.0 32.1 + - + +
1209A ILE* 1.3 80.7 - - - +
1211A ARG* 1.3 62.6 + - + +
1213A SER* 2.5 23.3 + - - -
1214A LYS* 4.1 8.8 + - - +
1218A GLN 5.3 1.1 - - - -
1219A ALA* 3.2 38.2 - - + +
1220A SER 4.2 10.0 + - - +
1222A VAL* 6.0 4.0 - - + -
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Residues in contact with ARG1211 (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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1207A VAL* 2.9 56.5 + - - +
1208A ALA* 3.2 12.1 - - - +
1210A THR* 1.3 82.0 - - - +
1212A ALA* 1.3 63.8 + - - +
1213A SER 3.1 0.3 + - - -
1214A LYS* 3.3 36.5 + - - +
4E GLU* 5.0 9.1 + - - -
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Residues in contact with ALA1212 (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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1208A ALA 2.9 13.3 + - - +
1209A ILE* 4.0 1.8 - - - +
1211A ARG* 1.3 72.5 - - - +
1213A SER* 1.3 60.8 + - - +
1214A LYS* 2.9 8.8 + - - +
1215A LEU* 3.2 28.9 + - + +
1217A ILE* 5.4 0.2 - - - +
1270A VAL* 4.7 16.0 - - + +
1271A VAL* 3.6 36.6 - - + +
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Residues in contact with SER1213 (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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1209A ILE* 2.6 23.2 + - - -
1210A THR* 2.5 33.5 + - - -
1211A ARG 3.1 0.2 - - - -
1212A ALA* 1.3 71.7 - - - +
1214A LYS* 1.3 53.9 + - - +
1215A LEU 3.0 0.4 - - - -
1216A LYS 2.7 11.0 + - - -
1217A ILE* 2.6 72.5 + - - +
1218A GLN 4.4 5.3 - - - -
1219A ALA* 4.7 0.7 + - - +
1270A VAL* 6.1 0.6 - - - +
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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