Contacts of the helix formed by residues 1190 - 1194 (chain D) in PDB entry 2O5J
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 SER1190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1118D ILE* 4.1 7.4 - - - -
1147D ARG* 3.7 15.3 - - - +
1188D VAL 3.4 6.0 + - - -
1189D ARG* 1.3 77.2 - - - +
1191D PRO* 1.3 76.6 - - - +
1192D LEU* 2.8 41.0 + - - +
1193D THR* 2.9 20.5 + - - -
1194D CYS 3.7 3.8 + - - -
1204D CYS* 3.7 9.8 + - - +
1369D GLU* 3.2 7.1 + - - -
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Residues in contact with PRO1191 (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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1190D SER* 1.3 90.1 - - - +
1192D LEU* 1.3 55.0 - - - +
1193D THR 3.1 6.3 + - - -
1194D CYS* 3.4 13.1 + - + +
1200D VAL* 4.1 18.6 - - + -
1204D CYS* 3.8 10.1 - - + +
1205D TYR* 3.9 17.7 - - + +
1366D LYS* 5.8 0.2 - - + -
1369D GLU* 3.3 16.4 - - - +
1370D ILE* 3.2 50.7 - - + +
1373D ARG* 3.1 26.2 - - - -
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Residues in contact with LEU1192 (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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1118D ILE* 3.4 33.4 - - + -
1190D SER* 2.9 23.1 - - - +
1191D PRO* 1.3 76.4 - - - +
1193D THR* 1.3 60.3 + - + +
1194D CYS 3.9 0.2 - - - -
1345D GLU* 2.9 55.6 - - + +
1346D ARG* 4.4 10.3 - - - +
1349D VAL* 4.6 1.8 - - + -
1369D GLU* 3.4 42.8 - - + +
1372D VAL* 3.6 10.1 - - + -
1373D ARG* 4.7 7.2 - - - +
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Residues in contact with THR1193 (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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1114D THR* 3.4 17.8 - - - +
1116D ASN* 2.5 36.3 + - + +
1117D TYR* 3.2 34.2 - - - +
1118D ILE* 4.2 3.5 + - + +
1190D SER* 2.9 15.1 + - - -
1192D LEU* 1.3 87.8 - - + +
1194D CYS* 1.3 64.3 + - - +
1204D CYS* 4.6 4.0 - - - -
1345D GLU* 4.6 3.1 - - - +
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Residues in contact with CYS1194 (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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1112D CYS* 4.3 0.2 - - - -
1114D THR* 4.0 1.5 - - - +
1190D SER 3.7 1.2 + - - -
1191D PRO* 3.4 16.1 + - + +
1192D LEU 3.9 0.2 - - - -
1193D THR* 1.3 81.0 - - - +
1195D GLN* 1.3 67.3 + - - +
1196D THR* 3.3 23.1 - - - +
1199D GLY 4.1 0.9 - - - -
1200D VAL* 3.9 10.5 - - + -
1201D CYS 3.8 12.8 - - - -
1204D CYS* 3.8 5.6 - - - -
1373D ARG* 3.9 15.2 - - - +
6112D ZN 2.4 39.3 - - - -
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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