Contacts of the helix formed by residues 1248 - 1262 (chain F) in PDB entry 5TJ4
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 ASN1248 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1247F ARG* 1.3 78.6 - - - +
1249F MET* 1.3 62.0 + - - +
1250F LYS* 2.4 42.8 + - - +
1251F GLU* 3.2 20.3 + - + +
1252F LYS* 3.0 26.0 + - - +
1372F GLU 3.9 17.4 + - - +
1373F LEU* 4.3 10.1 - - - +
1374F ALA* 4.1 15.6 - - + +
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Residues in contact with MET1249 (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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1247F ARG 3.8 1.2 + - - -
1248F ASN* 1.3 72.9 + - - +
1250F LYS* 1.3 71.8 + - - +
1251F GLU 3.1 1.6 - - - -
1252F LYS* 3.3 11.9 + - + +
1253F LEU* 3.1 24.0 + - + +
1366F MET* 4.2 6.5 - - + -
1372F GLU* 4.2 20.4 - - + -
1373F LEU 4.6 9.1 + - - +
1374F ALA* 5.0 1.2 - - - +
1390F CYS* 4.1 43.5 - - + +
1393F TYR* 3.5 35.0 - - + -
1394F VAL* 4.2 15.3 - - + +
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Residues in contact with LYS1250 (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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1248F ASN* 2.4 29.7 + - - +
1249F MET* 1.3 81.1 - - - +
1251F GLU* 1.3 60.1 + - - +
1253F LEU* 3.8 5.3 + - - +
1254F GLU* 3.1 34.0 + - + +
1372F GLU* 4.6 10.0 + - + +
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Residues in contact with GLU1251 (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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1248F ASN* 3.2 27.4 + - + +
1249F MET 3.1 0.4 - - - -
1250F LYS* 1.3 76.7 - - - +
1252F LYS* 1.3 66.9 + - - +
1254F GLU* 3.0 11.6 + - - +
1255F ASP* 2.9 29.0 + - - +
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Residues in contact with LYS1252 (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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1241F LEU 5.9 2.2 - - - +
1247F ARG 5.8 2.9 - - - +
1248F ASN 3.0 14.6 + - - +
1249F MET* 3.5 14.6 - - + +
1251F GLU* 1.3 74.5 - - - +
1253F LEU* 1.3 57.2 + - - +
1255F ASP* 3.3 8.7 + - - +
1256F MET* 3.0 39.3 + - + +
1331F ASP* 4.3 29.6 - - + +
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Residues in contact with LEU1253 (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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1249F MET* 3.1 17.1 + - + +
1250F LYS* 4.0 5.8 - - - +
1252F LYS* 1.3 76.8 - - - +
1254F GLU* 1.3 63.5 + - - +
1256F MET* 3.1 27.7 + - + +
1257F GLU* 2.8 54.0 + - + +
1359F LYS* 5.7 1.1 - - - +
1393F TYR* 3.7 33.7 - - + +
1394F VAL* 4.1 15.5 - - + -
1397F SER* 3.9 21.3 - - - +
1398F ILE* 3.9 19.3 - - + -
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Residues in contact with GLU1254 (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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1250F LYS* 3.1 25.1 + - - +
1251F GLU* 3.0 12.5 + - - +
1253F LEU* 1.3 84.1 - - - +
1255F ASP* 1.3 59.2 + - - +
1257F GLU* 4.0 16.7 - - - +
1258F SER* 3.1 29.5 + - - -
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Residues in contact with ASP1255 (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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1251F GLU* 2.9 22.8 + - - +
1252F LYS* 3.5 10.2 - - - +
1254F GLU* 1.3 75.4 - - - +
1256F MET* 1.3 67.8 + - + +
1258F SER* 3.1 7.8 + - - -
1259F VAL* 3.1 29.8 + - + +
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Residues in contact with MET1256 (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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1252F LYS* 3.0 21.4 + - + +
1253F LEU* 3.2 49.6 - - + +
1255F ASP* 1.3 76.3 - - + +
1257F GLU* 1.3 62.2 + - - +
1259F VAL* 3.3 3.3 + - - +
1260F LEU* 3.2 29.3 + - + +
1328F ALA* 4.2 26.9 - - + +
1331F ASP* 3.5 38.4 - - - +
1332F PHE* 4.5 5.8 - - - -
1394F VAL* 3.7 23.1 - - + -
1398F ILE* 3.8 15.3 - - + -
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Residues in contact with GLU1257 (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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1253F LEU* 2.8 41.7 + - + +
1254F GLU* 4.0 18.5 - - - +
1256F MET* 1.3 73.3 - - - +
1258F SER* 1.3 57.2 + - - +
1260F LEU* 3.5 5.1 + - - +
1261F LYS* 2.9 30.0 + - - +
1359F LYS* 4.3 8.9 + - - -
1397F SER* 3.9 22.0 - - - +
1398F ILE* 4.1 17.5 - - + -
1401F GLU* 4.3 15.5 - - + +
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Residues in contact with SER1258 (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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1254F GLU 3.1 18.6 + - - -
1255F ASP* 3.4 8.7 - - - -
1257F GLU* 1.3 74.3 - - - +
1259F VAL* 1.3 65.7 + - - +
1261F LYS* 3.6 10.9 + - - +
1262F ASP* 3.6 21.0 + - - +
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Residues in contact with VAL1259 (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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1255F ASP* 3.1 18.3 + - + +
1256F MET* 3.3 8.0 + - - +
1258F SER* 1.3 73.9 - - - +
1260F LEU* 1.3 67.5 + - + +
1262F ASP* 3.5 23.0 + - - +
1263F LEU* 4.0 3.6 - - - +
1322F VAL* 5.4 1.6 - - + -
1324F ALA* 3.9 26.9 - - + +
1325F ARG* 3.4 45.5 + - + +
1328F ALA* 4.6 3.8 - - + -
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Residues in contact with LEU1260 (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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1256F MET 3.2 18.1 + - - +
1257F GLU* 4.1 4.3 - - - +
1259F VAL* 1.3 79.0 - - + +
1261F LYS* 1.3 66.3 + - - +
1263F LEU* 3.5 33.3 - - + +
1268F ARG* 4.1 11.8 - - - +
1271F VAL* 5.5 3.6 - - + -
1325F ARG* 5.3 3.8 - - + +
1328F ALA* 4.5 18.2 - - + -
1329F ILE* 4.5 19.7 - - + -
1398F ILE* 3.7 35.9 - - + +
1401F GLU* 5.8 6.3 - - + -
1402F LEU* 4.0 28.0 - - + +
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Residues in contact with LYS1261 (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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1257F GLU 2.9 18.5 + - - +
1258F SER* 3.6 9.9 - - - +
1259F VAL 3.3 0.2 - - - -
1260F LEU* 1.3 78.0 - - - +
1262F ASP* 1.3 63.6 + - - +
1263F LEU* 2.9 11.8 + - - +
1268F ARG* 5.0 4.7 - - - +
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Residues in contact with ASP1262 (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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1258F SER* 3.6 13.8 + - - +
1259F VAL* 3.5 12.1 + - - +
1260F LEU 3.4 0.4 - - - -
1261F LYS* 1.3 78.2 - - - +
1263F LEU* 1.3 66.2 + - - +
1325F ARG* 4.0 12.3 + - - -
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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