Contacts of the helix formed by residues 1295 - 1307 (chain G) in PDB entry 4PKI
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 GLY1295 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1293G PRO* 3.3 7.7 - - - +
1294G LEU* 1.3 78.8 - - - +
1296G ASN* 1.3 67.5 + - - -
1297G LYS 3.2 3.4 - - - -
1298G VAL* 3.1 14.8 + - - -
1299G GLU* 3.1 16.4 + - - +
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Residues in contact with ASN1296 (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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1295G GLY* 1.3 71.7 - - - -
1297G LYS* 1.3 63.9 + - - +
1299G GLU* 3.4 15.3 + - - +
1300G MET* 3.3 30.0 + - + +
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Residues in contact with LYS1297 (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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1295G GLY 3.2 0.8 - - - -
1296G ASN* 1.3 78.1 - - - +
1298G VAL* 1.3 65.9 + - + +
1300G MET* 3.0 16.8 + - + +
1301G GLU* 3.0 47.8 + - + +
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Residues in contact with VAL1298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1266G GLY* 3.5 37.9 - - - +
1267G ALA* 4.8 0.7 - - - +
1270G LEU* 4.5 9.4 - - + -
1294G LEU* 3.3 28.3 - - + +
1295G GLY* 3.1 2.6 + - - +
1297G LYS* 1.3 75.7 - - + +
1299G GLU* 1.3 64.0 + - - +
1301G GLU* 3.0 17.0 + - - +
1302G ILE* 2.9 48.6 + - + +
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Residues in contact with GLU1299 (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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1294G LEU* 4.9 13.4 - - + +
1295G GLY 3.1 20.3 + - - +
1296G ASN* 3.6 16.7 - - - +
1297G LYS 3.4 0.2 - - - -
1298G VAL* 1.3 75.8 - - - +
1300G MET* 1.3 63.9 + - + +
1302G ILE* 3.4 12.6 + - + +
1303G VAL* 3.2 26.9 + - - +
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Residues in contact with MET1300 (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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1296G ASN* 3.3 18.5 + - + +
1297G LYS* 3.0 13.6 + - + +
1298G VAL 3.0 0.6 - - - -
1299G GLU* 1.3 77.8 - - + +
1301G GLU* 1.3 65.7 - - + +
1302G ILE 3.0 1.3 - - - -
1303G VAL* 3.2 15.8 - - + +
1304G SER* 3.1 22.6 + - - -
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Residues in contact with GLU1301 (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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1270G LEU* 3.5 37.1 - - + +
1297G LYS* 3.0 50.9 - - + +
1298G VAL* 3.0 11.4 + - - +
1300G MET* 1.3 76.6 - - + +
1302G ILE* 1.3 58.8 + - - +
1304G SER* 2.6 26.4 + - - +
1305G MET* 3.3 13.2 + - - +
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Residues in contact with ILE1302 (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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1269G ILE* 3.9 13.2 - - + -
1270G LEU* 4.3 4.0 - - + -
1273G VAL* 4.1 32.9 - - + +
1287G ILE* 5.2 2.0 - - + -
1294G LEU* 3.9 21.5 - - + -
1298G VAL* 2.9 41.7 + - + +
1299G GLU* 3.5 10.5 - - + +
1300G MET 3.0 0.2 - - - -
1301G GLU* 1.3 76.5 - - - +
1303G VAL* 1.3 69.5 + - + +
1305G MET* 3.1 5.9 + - - +
1306G LEU* 2.9 35.5 + - + +
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Residues in contact with VAL1303 (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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1299G GLU 3.2 12.5 + - - +
1300G MET* 3.2 29.2 - - + +
1302G ILE* 1.3 81.2 - - + +
1304G SER* 1.3 65.0 + - - +
1306G LEU* 3.0 19.8 + - + +
1307G GLU 3.0 19.6 + - - -
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Residues in contact with SER1304 (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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1300G MET 3.1 13.4 + - - -
1301G GLU* 2.6 25.3 + - - -
1303G VAL* 1.3 80.8 - - - +
1305G MET* 1.3 67.4 + - - +
1307G GLU 3.4 6.2 + - - -
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Residues in contact with MET1305 (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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1270G LEU* 4.8 1.1 - - + -
1273G VAL* 3.7 34.5 - - + +
1274G GLU* 4.0 23.6 - - + +
1276G LEU* 4.8 8.9 - - - +
1277G PRO* 3.3 42.9 - - + +
1301G GLU 3.4 13.5 - - - +
1302G ILE 3.1 8.1 + - - +
1304G SER* 1.3 86.3 + - - +
1306G LEU* 1.3 68.1 + - - +
1307G GLU 3.3 0.3 + - - -
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Residues in contact with LEU1306 (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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1273G VAL* 5.0 6.7 - - + -
1276G LEU* 3.8 25.8 - - + -
1302G ILE* 2.9 31.9 + - + +
1303G VAL* 3.0 20.6 + - + +
1305G MET* 1.3 77.7 - - - +
1307G GLU 1.3 48.0 + - - +
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Residues in contact with GLU1307 (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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1303G VAL 3.0 13.3 + - - -
1304G SER 3.4 6.5 + - - -
1305G MET 3.2 4.8 + - - -
1306G LEU* 1.3 67.5 + - - +
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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