Contacts of the helix formed by residues 1248 - 1262 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1247G ARG* 1.3 75.8 - - - +
1249G MET* 1.3 60.7 + - - +
1250G LYS* 2.5 38.4 + - - +
1251G GLU* 3.4 18.6 - - + +
1252G LYS* 3.0 25.7 + - - +
1373G LEU 3.0 11.7 + - - +
1374G ALA* 2.8 36.1 - - + +
1375G SER 5.0 10.1 - - - +
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Residues in contact with MET1249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247G ARG 3.9 0.6 + - - -
1248G ASN* 1.3 73.0 + - - +
1250G LYS* 1.3 65.3 + - - +
1251G GLU 3.1 1.3 - - - -
1252G LYS* 3.1 15.0 + - - +
1253G LEU* 3.0 23.1 + - + +
1372G GLU 5.9 1.6 - - - +
1373G LEU 4.7 4.9 + - - +
1375G SER 5.2 4.9 + - - +
1390G CYS* 4.4 35.0 - - + -
1393G TYR* 6.5 0.7 - - + -
1394G VAL* 4.4 22.9 - - + -
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Residues in contact with LYS1250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248G ASN* 2.5 22.3 + - - +
1249G MET* 1.3 74.8 - - - +
1251G GLU* 1.3 60.1 + - - +
1253G LEU* 3.8 8.9 + - - +
1254G GLU* 3.2 31.8 + - - +
1373G LEU* 3.3 29.2 + - + +
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Residues in contact with GLU1251 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247G ARG* 5.1 5.4 - - + -
1248G ASN* 3.2 30.6 + - + +
1249G MET 3.1 0.4 - - - -
1250G LYS* 1.3 75.1 - - - +
1252G LYS* 1.3 66.2 + - - +
1254G GLU* 3.0 17.6 + - - +
1255G ASP* 2.9 29.1 + - - +
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Residues in contact with LYS1252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247G ARG* 5.4 6.9 - - + +
1248G ASN 3.0 14.0 + - - +
1249G MET* 3.1 20.8 + - - +
1251G GLU* 1.3 74.7 - - - +
1253G LEU* 1.3 58.1 + - - +
1255G ASP* 3.3 9.4 + - - +
1256G MET* 3.0 39.6 + - - +
1331G ASP* 5.6 4.5 - - - +
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Residues in contact with LEU1253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249G MET* 3.0 14.8 + - + +
1250G LYS* 4.0 7.2 - - - +
1252G LYS* 1.3 72.7 - - - +
1254G GLU* 1.3 59.2 + - - +
1256G MET* 3.1 7.0 + - - -
1257G GLU* 2.8 53.0 + - + +
1393G TYR* 3.7 33.2 - - + +
1394G VAL* 4.1 26.5 - - + -
1397G SER* 3.9 21.5 - - - +
1398G ILE* 3.9 26.9 - - + -
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Residues in contact with GLU1254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250G LYS* 3.2 21.7 + - - +
1251G GLU* 3.0 17.9 + - - +
1253G LEU* 1.3 78.1 - - + +
1255G ASP* 1.3 64.4 + - - +
1257G GLU* 3.6 9.9 + - - +
1258G SER* 3.1 24.1 + - - -
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Residues in contact with ASP1255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251G GLU* 2.9 21.1 + - - +
1252G LYS* 3.5 9.7 - - - +
1254G GLU* 1.3 76.7 - - - +
1256G MET* 1.3 65.9 + - + +
1258G SER* 3.2 8.0 + - - -
1259G VAL* 3.1 29.0 + - + +
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Residues in contact with MET1256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252G LYS* 3.0 27.5 + - - +
1253G LEU* 3.1 10.1 + - - +
1255G ASP* 1.3 76.2 - - + +
1257G GLU* 1.3 62.1 + - - +
1259G VAL* 3.3 4.8 + - - +
1260G LEU* 3.2 29.6 + - + +
1328G ALA* 3.4 29.1 - - + +
1331G ASP* 3.5 26.9 - - + +
1332G PHE* 3.4 38.8 - - + +
1394G VAL* 4.2 14.1 - - + -
1398G ILE* 3.8 26.5 - - + -
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Residues in contact with GLU1257 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253G LEU* 2.8 43.9 + - + +
1254G GLU* 4.0 7.6 + - - +
1256G MET* 1.3 72.2 - - - +
1258G SER* 1.3 59.6 + - - +
1260G LEU* 3.5 4.8 + - - +
1261G LYS* 2.9 30.1 + - - +
1397G SER* 3.9 22.3 - - - +
1398G ILE* 4.1 18.2 - - + -
1401G GLU* 4.3 16.4 - - + +
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Residues in contact with SER1258 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254G GLU 3.1 18.6 + - - -
1255G ASP* 3.2 9.2 + - - -
1257G GLU* 1.3 74.5 - - - +
1259G VAL* 1.3 66.4 + - - +
1261G LYS* 3.6 12.0 + - - +
1262G ASP* 3.6 19.9 + - - +
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Residues in contact with VAL1259 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1255G ASP* 3.1 18.6 + - + +
1256G MET* 3.3 8.0 + - - +
1258G SER* 1.3 75.1 - - - +
1260G LEU* 1.3 67.4 + - + +
1261G LYS 3.5 0.3 + - - -
1262G ASP* 3.5 21.9 + - - +
1263G LEU* 4.1 4.0 - - - +
1322G VAL* 5.4 1.8 - - + -
1324G ALA* 3.9 27.6 - - + +
1325G ARG* 3.4 46.3 + - + +
1328G ALA* 4.7 4.3 - - + -
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Residues in contact with LEU1260 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256G MET* 3.2 18.0 + - + +
1257G GLU* 4.1 4.7 - - - +
1258G SER 3.4 0.2 - - - -
1259G VAL* 1.3 84.6 - - + +
1261G LYS* 1.3 66.0 + - - +
1263G LEU* 3.5 29.8 - - + +
1268G ARG* 3.5 17.1 + - - +
1271G VAL* 5.5 2.9 - - + -
1325G ARG* 5.3 4.0 - - + +
1328G ALA* 4.5 14.1 - - + -
1329G ILE* 4.5 19.1 - - + -
1398G ILE* 3.7 36.6 - - + +
1401G GLU* 5.7 7.4 - - + -
1402G LEU* 4.0 26.9 - - + -
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Residues in contact with LYS1261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257G GLU 2.9 19.0 + - - +
1258G SER* 3.6 10.5 - - - +
1259G VAL 3.3 0.2 - - - -
1260G LEU* 1.3 75.9 - - - +
1262G ASP* 1.3 62.8 + - - +
1263G LEU 2.8 9.7 + - - +
1268G ARG* 3.4 29.1 + - - +
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Residues in contact with ASP1262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258G SER* 3.6 13.0 + - - +
1259G VAL* 3.5 12.5 + - - +
1260G LEU 3.4 0.6 - - - -
1261G LYS* 1.3 77.4 - - - +
1263G LEU* 1.3 65.2 + - - +
1325G ARG* 3.9 13.3 + - - -
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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