Contacts of the helix formed by residues 1205 - 1209 (chain A) in PDB entry 3F2B
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 THR1205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1199A ILE* 4.2 4.9 - - - -
1204A CYS* 1.3 82.0 - - - +
1206A LEU* 1.3 65.5 + - - +
1207A SER* 3.3 15.4 + - - -
1208A GLU* 3.1 42.4 + - - +
1209A VAL* 3.3 13.2 + - - +
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Residues in contact with LEU1206 (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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1170A THR* 4.1 44.0 - - + +
1177A GLU* 5.9 8.3 - - + -
1180A GLN* 2.9 28.2 - - + +
1181A ILE* 5.0 5.8 - - + -
1184A LEU* 4.4 18.6 - - + -
1191A TRP* 4.5 0.4 - - + -
1199A ILE* 3.7 34.9 - - + +
1205A THR* 1.3 75.3 - - - +
1207A SER* 1.3 61.5 + - - +
1208A GLU 3.4 0.2 + - - -
1209A VAL* 3.6 5.4 + - - +
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Residues in contact with SER1207 (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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1180A GLN* 3.7 16.2 + - - +
1205A THR* 3.2 12.5 + - - -
1206A LEU* 1.3 83.1 - - - +
1208A GLU* 1.3 61.1 + - - +
1209A VAL 3.4 2.5 + - - +
1215A ASP* 5.5 2.8 - - - +
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Residues in contact with GLU1208 (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 CYS* 3.3 27.0 - - + +
1205A THR* 3.1 33.8 + - - +
1207A SER* 1.3 79.1 - - - +
1209A VAL* 1.3 66.5 + - - +
1210A ILE* 3.8 2.8 + - - +
1259A TRP* 4.2 16.3 - - + -
1260A TYR* 5.1 3.8 - - - -
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Residues in contact with VAL1209 (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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1180A GLN* 3.4 14.9 + - - +
1184A LEU* 3.4 33.4 - - + -
1195A ALA* 3.4 41.5 - - + +
1198A LEU* 4.3 7.9 - - + -
1199A ILE* 3.8 17.0 - - + -
1204A CYS* 4.0 15.3 - - - -
1205A THR 3.3 3.5 + - - +
1206A LEU 3.6 8.7 - - - +
1207A SER 3.4 3.0 - - - +
1208A GLU* 1.3 82.4 - - - +
1210A ILE* 1.3 63.6 + - - +
1211A GLY 3.2 7.4 + - - -
1215A ASP* 5.1 3.6 - - - +
1259A TRP* 5.5 0.9 - - - -
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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