Contacts of the helix formed by residues 1197 - 1210 (chain F) in PDB entry 5TWV
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 GLN1197 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1193F ASP 4.4 4.2 + - - +
1194F ASP 4.0 9.8 + - - +
1195F THR 3.3 2.8 - - - -
1196F THR* 1.3 79.4 - - - +
1198F LEU* 1.3 64.8 + - - +
1200F LEU* 3.2 22.7 + - - +
1201F VAL* 3.8 3.5 + - - +
1234F ASN* 4.2 7.2 - - - +
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Residues in contact with LEU1198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195F THR 4.4 4.3 + - - +
1197F GLN* 1.3 77.6 - - - +
1199F PRO* 1.4 67.7 - - + +
1201F VAL* 3.3 9.1 + - - +
1202F SER* 3.0 20.3 + - - -
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Residues in contact with PRO1199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195F THR 4.2 6.5 - - - +
1196F THR* 3.7 13.0 - - - +
1197F GLN 3.6 3.8 - - - -
1198F LEU* 1.4 92.5 - - + +
1200F LEU* 1.3 56.5 + - - +
1202F SER* 3.2 11.0 + - - -
1203F HIS* 3.0 34.6 + - - +
1230F TYR* 4.8 16.2 - - + -
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Residues in contact with LEU1200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196F THR 4.8 0.8 + - - -
1197F GLN 3.2 13.4 + - - +
1198F LEU 3.2 0.4 - - - -
1199F PRO* 1.3 79.2 - - - +
1201F VAL* 1.3 57.0 + - - +
1203F HIS* 3.3 17.2 + - - +
1204F PHE* 2.9 50.0 + - + -
1230F TYR* 5.2 5.0 - - + -
1234F ASN* 3.7 23.8 - - - +
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Residues in contact with VAL1201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422F ALA* 5.8 5.8 - - + -
1197F GLN 3.8 3.6 + - - +
1198F LEU* 3.3 10.6 + - - +
1200F LEU* 1.3 76.0 - - - +
1202F SER* 1.3 59.8 + - - +
1204F PHE* 3.4 15.9 - - + +
1205F ALA* 2.9 28.4 + - - +
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Residues in contact with SER1202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781F ASN* 4.8 18.0 - - - +
1198F LEU 3.0 13.4 + - - -
1199F PRO* 3.2 16.3 + - - -
1201F VAL* 1.3 76.5 - - - +
1203F HIS* 1.3 58.3 + - - +
1205F ALA* 3.2 8.5 + - - +
1206F GLU* 3.0 24.1 + - - +
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Residues in contact with HIS1203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1199F PRO 3.0 28.9 + - - +
1200F LEU* 3.3 14.1 - - + -
1202F SER* 1.3 74.1 - - - +
1204F PHE* 1.3 87.0 + + - +
1206F GLU* 3.7 11.4 - - + -
1207F THR* 2.9 25.5 + - - -
1223F PHE* 3.2 30.6 - + + -
1227F LEU* 3.5 15.5 - - + -
1230F TYR* 3.2 50.9 - + + +
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Residues in contact with PHE1204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392F GLN* 5.8 3.8 - - + -
396F TYR* 3.2 53.7 - + + +
418F CYS* 4.8 13.3 - - + +
422F ALA* 4.9 15.7 - - + -
1200F LEU* 2.9 32.7 + - + -
1201F VAL* 3.4 18.6 - - + +
1202F SER 3.1 0.4 - - - -
1203F HIS* 1.3 101.0 - + - +
1205F ALA* 1.3 59.5 + - - +
1207F THR* 3.1 5.9 + - - -
1208F VAL* 2.9 27.9 + - - +
1227F LEU* 3.6 12.6 - - + -
1231F THR* 6.2 4.7 - - - -
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Residues in contact with ALA1205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418F CYS* 6.0 0.9 - - - -
825F GLU* 5.7 9.2 - - + -
1201F VAL 2.9 13.3 + - - +
1202F SER* 3.6 9.6 - - - +
1204F PHE* 1.3 74.1 - - - +
1206F GLU* 1.3 58.5 + - - +
1208F VAL* 3.3 7.0 + - - +
1209F GLU* 2.9 30.1 + - - +
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Residues in contact with GLU1206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780F LEU* 4.8 11.0 - - + +
781F ASN* 4.5 21.5 - - + +
1202F SER 3.0 17.1 + - - +
1203F HIS* 3.8 12.6 - - + +
1205F ALA* 1.3 76.1 - - - +
1207F THR* 1.3 61.9 + - - +
1209F GLU* 4.0 5.8 - - - +
1210F GLY* 3.1 22.3 + - - -
1223F PHE* 5.8 2.2 - - + -
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Residues in contact with THR1207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396F TYR* 4.8 13.0 - - - -
1203F HIS 2.9 20.7 + - - -
1204F PHE* 3.1 10.5 + - - -
1206F GLU* 1.3 79.1 - - - +
1208F VAL* 1.3 59.8 + - - +
1210F GLY 4.4 0.9 - - - -
1211F LEU* 4.2 16.1 + - - +
1223F PHE* 3.7 26.2 - - - -
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Residues in contact with VAL1208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414F ALA* 5.0 6.0 - - + +
415F GLY* 4.7 14.8 - - - +
418F CYS* 4.7 16.4 - - + -
1204F PHE 2.9 15.0 + - - +
1205F ALA* 3.3 7.2 + - - +
1206F GLU 3.3 0.2 - - - -
1207F THR* 1.3 76.3 - - - +
1209F GLU* 1.3 63.4 + - - +
1211F LEU* 4.1 10.9 + - - +
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Residues in contact with GLU1209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778F TRP* 5.0 18.6 - - + +
779F LEU 5.0 10.8 - - - +
1205F ALA 2.9 17.7 + - - +
1206F GLU* 4.0 6.3 - - - +
1207F THR 3.3 0.2 - - - -
1208F VAL* 1.3 80.3 - - - +
1210F GLY* 1.3 59.2 + - - +
1211F LEU* 3.1 6.6 + - - +
1212F THR 4.8 1.2 + - - -
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Residues in contact with GLY1210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778F TRP* 5.8 3.8 - - - -
1206F GLU 3.1 12.6 + - - -
1207F THR 4.4 3.8 - - - -
1209F GLU* 1.3 77.6 - - - +
1211F LEU* 1.3 52.5 + - - +
1212F THR 3.4 2.0 - - - -
1213F THR* 3.2 18.7 + - - -
1214F ILE* 2.7 31.5 + - - +
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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