Contacts of the helix formed by residues 1232 - 1236 (chain D) in PDB entry 4OIR
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 PRO1232 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1228D SER 3.2 20.6 - - - +
1229D ILE 3.5 14.4 - - - +
1231D GLU* 1.3 104.4 - - - +
1233D GLY* 1.3 52.2 + - - +
1234D THR 3.1 0.4 - - - -
1235D GLN* 2.7 43.8 + - - +
1236D LEU* 3.8 6.3 + - - +
1356D TYR* 3.6 17.5 - - + -
1361D VAL* 3.6 38.8 - - + -
1363D LEU* 4.9 0.9 - - + -
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Residues in contact with GLY1233 (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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1087D ARG 5.4 0.2 - - - +
1091D SER* 3.4 15.6 + - - -
1094D LEU* 6.2 1.8 - - - -
1229D ILE 4.1 4.2 + - - -
1230D GLY* 3.0 17.4 + - - -
1232D PRO* 1.3 79.4 - - - +
1234D THR* 1.3 58.8 + - - +
1235D GLN 3.1 0.9 + - - -
1236D LEU* 3.2 34.3 + - - +
1256D LEU* 4.1 12.8 - - - +
1356D TYR* 4.7 2.2 - - - -
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Residues in contact with THR1234 (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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708D LEU* 4.5 19.5 - - + +
1084D THR* 6.0 0.2 - - - +
1087D ARG* 3.1 32.2 + - - +
1088D THR* 4.9 18.8 - - + +
1091D SER* 3.3 25.4 - - - +
1230D GLY 4.9 0.9 - - - +
1231D GLU 4.0 13.5 + - - +
1232D PRO 2.9 0.8 + - - -
1233D GLY* 1.3 74.6 - - - +
1235D GLN* 1.3 63.1 + - - +
1236D LEU 3.4 1.3 - - - -
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Residues in contact with GLN1235 (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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1087D ARG* 4.0 11.0 + - - +
1231D GLU* 4.2 17.8 + - - -
1232D PRO* 2.7 23.0 + - + +
1234D THR* 1.3 86.6 - - - +
1236D LEU* 1.3 64.0 + - + +
1237D THR 4.2 0.3 + - - -
1359D GLN* 3.6 25.7 - - + +
1361D VAL* 3.7 19.3 - - + +
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Residues in contact with LEU1236 (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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1087D ARG* 3.1 23.7 - - - +
1232D PRO 3.9 10.1 - - - +
1233D GLY* 3.2 21.4 + - - +
1235D GLN* 1.3 84.5 - - + +
1237D THR* 1.3 63.1 + - - +
1255D GLY* 4.4 4.0 - - - -
1256D LEU* 3.7 25.0 - - + +
1259D VAL* 4.2 8.1 - - + -
1355D VAL* 3.8 22.4 - - + +
1356D TYR* 3.7 38.4 - - + +
1359D GLN* 3.5 33.4 - - + -
1361D VAL* 5.1 2.7 - - + -
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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