Contacts of the helix formed by residues 1193 - 1203 (chain B) in PDB entry 3PT6
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 ASP1193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1172B MET* 3.8 21.4 - - + +
1192B GLU* 1.3 78.8 - - - +
1194B CYS* 1.3 62.3 + - - +
1195B ASN* 3.0 43.0 + - - +
1196B VAL* 2.9 32.0 + - + +
1197B LEU* 3.1 8.4 + - - +
1250B LEU* 4.8 0.3 - - - +
1603B SAH 2.6 31.8 + - - -
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Residues in contact with CYS1194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147B VAL* 4.4 8.1 - - + -
1148B PHE* 3.8 23.8 - - - -
1170B ILE* 4.3 15.5 - - + -
1192B GLU 3.7 1.4 + - - -
1193B ASP* 1.3 71.4 - - - +
1195B ASN* 1.3 70.5 + - - +
1197B LEU* 4.0 4.0 - - - -
1198B LEU* 2.9 18.2 + - - +
1250B LEU* 4.4 4.3 - - - -
1253B SER* 4.5 10.1 - - - -
1257B TYR* 2.6 42.3 + - + +
1603B SAH 3.6 21.2 + - - +
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Residues in contact with ASN1195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193B ASP* 3.0 24.9 + - - +
1194B CYS* 1.3 78.2 - - - +
1196B VAL* 1.3 63.6 + - - +
1198B LEU* 3.1 8.5 + - - +
1199B LYS* 3.0 22.4 + - - +
1248B ASN 5.4 4.4 + - - +
1250B LEU* 4.2 15.4 - - - +
1253B SER* 2.7 31.9 + - - -
1257B TYR* 5.5 0.4 - - - -
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Residues in contact with VAL1196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192B GLU* 3.7 25.4 - - + +
1193B ASP* 2.9 36.7 + - + +
1195B ASN* 1.3 75.9 - - - +
1197B LEU* 1.3 61.1 + - - +
1199B LYS* 3.5 8.4 + - + +
1200B LEU* 3.2 34.8 + - + +
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Residues in contact with LEU1197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1170B ILE* 3.4 35.4 - - + -
1190B PHE* 3.5 35.7 - - + -
1192B GLU* 4.6 12.3 - - + -
1193B ASP 3.1 11.3 + - - +
1194B CYS 3.4 9.4 - - - +
1195B ASN 3.1 0.6 - - - -
1196B VAL* 1.3 77.2 - - + +
1198B LEU* 1.3 65.5 + - - +
1200B LEU* 3.3 24.4 + - + +
1201B VAL* 3.4 15.0 + - + +
1208B ASN* 5.0 4.7 - - + +
1214B LEU* 4.1 26.4 - - + +
1215B PRO* 6.3 2.2 - - + -
1257B TYR* 3.6 5.4 - - + +
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Residues in contact with LEU1198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1194B CYS 2.9 17.2 + - - +
1195B ASN* 3.6 6.7 - - - +
1197B LEU* 1.3 73.8 - - - +
1199B LYS* 1.3 67.7 + - - +
1201B VAL* 3.0 30.3 - - + +
1202B MET* 3.0 38.2 + - + +
1253B SER* 4.6 2.2 - - - +
1256B SER* 3.8 32.1 - - - +
1257B TYR* 3.5 25.3 + - + +
1260B TYR* 4.5 17.5 - - + -
1261B TYR* 4.6 11.0 - - + -
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Residues in contact with LYS1199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195B ASN 3.0 13.2 + - - +
1196B VAL* 3.7 13.0 - - + +
1198B LEU* 1.3 77.4 - - - +
1200B LEU* 1.3 53.1 + - + +
1202B MET* 3.0 11.1 + - - +
1203B ALA* 2.6 36.8 + - - +
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Residues in contact with LEU1200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196B VAL* 3.2 26.7 - - + +
1197B LEU* 3.5 16.2 - - + +
1198B LEU 3.2 0.4 - - - -
1199B LYS* 1.3 78.3 - - + +
1201B VAL* 1.3 58.8 + - - +
1203B ALA* 2.9 21.9 + - + -
1205B GLU* 3.1 37.8 + - + +
1207B THR 4.9 1.8 - - - +
1208B ASN* 4.5 27.4 - - + -
1209B SER 5.5 0.9 - - - +
1214B LEU* 4.1 9.9 - - + -
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Residues in contact with VAL1201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197B LEU* 3.4 12.8 + - + +
1198B LEU* 3.0 32.3 - - + +
1200B LEU* 1.3 76.0 - - - +
1202B MET* 1.3 57.7 + - - +
1204B GLY* 3.7 9.4 + - - -
1205B GLU 4.2 5.8 - - - +
1214B LEU* 4.0 20.1 - - + +
1215B PRO* 3.5 13.7 - - + +
1216B GLN* 4.0 14.8 + - - +
1257B TYR* 5.8 0.9 - - + -
1260B TYR* 3.6 25.8 + - + +
1261B TYR* 3.4 27.8 - - - +
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Residues in contact with MET1202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851B GLY* 3.7 31.2 - - - +
1198B LEU* 3.0 43.3 + - + +
1199B LYS* 3.3 10.5 - - - +
1201B VAL* 1.3 76.7 - - - +
1203B ALA* 1.3 56.7 + - - +
1204B GLY* 2.9 10.9 + - - -
1260B TYR* 4.3 22.0 - - + -
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Residues in contact with ALA1203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199B LYS 2.6 19.5 + - - +
1200B LEU* 2.9 14.0 + - + +
1202B MET* 1.3 71.1 - - - +
1204B GLY* 1.3 54.9 + - - +
1205B GLU* 3.0 18.9 + - + +
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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