Contacts of the helix formed by residues 1248 - 1262 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1247J ARG* 1.3 80.1 - - - +
1249J MET* 1.3 61.4 + - - +
1250J LYS* 2.4 43.9 + - - +
1251J GLU* 3.4 30.8 + - - +
1252J LYS* 3.0 26.0 + - - +
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Residues in contact with MET1249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241J LEU* 4.5 22.2 - - + -
1242J GLY* 5.3 7.2 - - - -
1247J ARG 3.9 1.0 + - - -
1248J ASN* 1.3 73.2 + - - +
1250J LYS* 1.3 62.3 + - - +
1251J GLU 3.2 1.1 - - - -
1252J LYS* 3.3 15.0 + - + +
1253J LEU* 3.1 24.4 + - - +
1390J CYS* 4.7 27.1 - - + -
1394J VAL* 5.3 11.0 - - + +
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Residues in contact with LYS1250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248J ASN* 2.4 29.5 + - - +
1249J MET* 1.3 69.3 - - - +
1251J GLU* 1.3 59.4 + - + +
1253J LEU* 3.8 6.4 + - - +
1254J GLU* 3.2 22.2 + - - +
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Residues in contact with GLU1251 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247J ARG* 3.5 18.6 - - + +
1248J ASN* 3.2 41.4 + - + +
1249J MET 3.2 0.6 - - - -
1250J LYS* 1.3 75.1 - - + +
1252J LYS* 1.3 66.6 + - - +
1254J GLU* 3.0 11.3 + - - +
1255J ASP* 2.9 28.0 + - - +
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Residues in contact with LYS1252 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241J LEU* 4.9 9.6 - - + -
1242J GLY* 4.5 25.6 - - - +
1245J ASP* 5.4 2.9 - - - +
1247J ARG* 3.9 38.0 + - + +
1248J ASN 3.0 14.6 + - - +
1249J MET* 3.5 20.2 - - + +
1251J GLU* 1.3 73.7 - - - +
1253J LEU* 1.3 57.2 + - - +
1255J ASP* 3.3 4.7 + - - +
1256J MET* 3.0 37.1 + - - +
1327J LYS* 5.3 2.9 - - - +
1331J ASP* 4.5 20.9 - - + +
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Residues in contact with LEU1253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249J MET 3.1 16.0 + - - +
1250J LYS* 4.1 6.5 - - - +
1252J LYS* 1.3 74.0 - - - +
1254J GLU* 1.3 58.7 + - - +
1256J MET* 3.1 9.1 + - - +
1257J GLU* 2.8 73.3 + - + +
1359J LYS* 5.9 0.9 - - - +
1393J TYR* 4.3 17.9 - - + +
1394J VAL* 3.4 50.9 - - + +
1397J SER* 3.9 19.5 - - - +
1398J ILE* 4.8 5.2 - - + -
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Residues in contact with GLU1254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1250J LYS 3.2 13.7 + - - +
1251J GLU* 3.0 14.1 + - - +
1253J LEU* 1.3 79.3 - - - +
1255J ASP* 1.3 60.0 + - - +
1257J GLU* 4.0 8.9 - - - +
1258J SER* 3.1 28.8 + - - -
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Residues in contact with ASP1255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247J ARG* 2.3 38.3 + - - +
1251J GLU* 2.9 16.3 + - - +
1252J LYS 3.5 7.9 - - - +
1254J GLU* 1.3 75.8 - - - +
1256J MET* 1.3 66.4 + - + +
1258J SER* 3.1 8.7 + - - -
1259J VAL* 3.1 29.0 + - + +
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Residues in contact with MET1256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1252J LYS* 3.0 28.8 + - - +
1253J LEU* 3.1 10.3 + - - +
1255J ASP* 1.3 74.9 - - + +
1257J GLU* 1.3 62.6 + - - +
1259J VAL* 3.3 4.4 + - - +
1260J LEU* 3.2 29.3 + - + +
1328J ALA* 3.4 29.3 - - + +
1331J ASP* 3.5 27.1 - - - +
1332J PHE* 3.3 39.5 - - + +
1394J VAL* 4.2 13.2 - - + -
1398J ILE* 3.8 26.2 - - + -
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Residues in contact with GLU1257 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253J LEU* 2.8 47.1 + - + +
1254J GLU* 4.0 6.4 + - - +
1256J MET* 1.3 73.7 - - - +
1258J SER* 1.3 57.1 + - - +
1260J LEU* 3.5 4.1 + - - +
1261J LYS* 2.9 31.2 + - - +
1359J LYS* 4.3 9.1 + - - -
1397J SER* 3.9 22.6 - - - +
1398J ILE* 4.1 17.0 - - + -
1401J GLU* 3.8 30.5 - - + +
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Residues in contact with SER1258 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254J GLU 3.1 19.0 + - - -
1255J ASP* 3.1 8.7 + - - -
1257J GLU* 1.3 74.5 - - - +
1259J VAL* 1.3 64.9 + - - +
1261J LYS* 3.6 11.6 + - - +
1262J ASP* 3.6 13.0 + - - +
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Residues in contact with VAL1259 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1255J ASP* 3.1 17.7 + - + +
1256J MET* 3.3 8.0 + - - +
1258J SER* 1.3 78.7 - - - +
1260J LEU* 1.3 65.7 + - + +
1262J ASP* 3.5 20.4 + - - +
1263J LEU* 4.1 3.6 - - - +
1322J VAL* 5.4 1.8 - - + -
1324J ALA* 3.9 28.0 - - + +
1325J ARG* 3.4 45.4 + - + +
1328J ALA* 4.6 4.3 - - + -
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Residues in contact with LEU1260 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256J MET* 3.2 17.5 + - + +
1257J GLU* 4.1 4.7 - - - +
1259J VAL* 1.3 82.4 - - + +
1261J LYS* 1.3 66.4 + - - +
1263J LEU* 3.5 23.2 - - + +
1268J ARG* 3.4 22.5 - - - -
1271J VAL* 5.5 2.9 - - + -
1325J ARG* 5.3 4.3 - - + +
1328J ALA* 4.5 14.6 - - + -
1329J ILE* 4.5 19.5 - - + -
1398J ILE* 3.7 36.1 - - + +
1401J GLU* 4.9 10.5 - - + -
1402J LEU* 4.0 27.8 - - + -
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Residues in contact with LYS1261 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257J GLU 2.9 18.5 + - - +
1258J SER* 3.6 9.4 - - - +
1260J LEU* 1.3 77.2 - - - +
1262J ASP* 1.3 57.5 + - - +
1263J LEU 2.8 13.2 + - - +
1268J ARG* 4.6 5.1 + - - +
1401J GLU* 4.0 15.2 + - - +
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Residues in contact with ASP1262 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1258J SER 3.6 6.8 + - - +
1259J VAL* 3.5 13.0 + - - +
1260J LEU 3.4 0.4 - - - -
1261J LYS* 1.3 74.4 - - - +
1263J LEU* 1.3 66.0 + - - +
1325J ARG* 3.9 13.0 + - - -
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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