Contacts of the helix formed by residues 1265 - 1275 (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 SER1265 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1238G ASP* 2.9 31.7 + - - -
1263G PHE 3.8 2.6 + - - -
1264G ILE* 1.3 77.2 - - - +
1266G GLY* 1.3 58.9 + - - +
1267G ALA* 3.0 18.5 + - - +
1268G GLY 3.0 2.3 + - - -
1269G ILE* 2.9 28.3 + - - +
1292G GLN* 5.7 7.4 - - - -
1294G LEU* 4.5 1.3 - - - -
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Residues in contact with GLY1266 (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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1265G SER* 1.3 74.4 - - - +
1267G ALA* 1.3 56.5 + - - +
1269G ILE* 4.4 1.1 - - - -
1270G LEU* 2.8 31.2 + - - +
1293G PRO 5.4 1.4 + - - -
1294G LEU* 3.9 35.9 + - - +
1298G VAL* 3.5 23.1 - - - +
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Residues in contact with ALA1267 (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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1238G ASP* 4.4 1.8 - - - +
1242G TYR* 3.7 20.1 - - - +
1265G SER* 3.0 9.7 + - - +
1266G GLY* 1.3 76.8 - - - +
1268G GLY* 1.3 61.7 + - - +
1270G LEU* 3.4 8.9 + - - +
1271G ARG* 3.0 24.6 + - - +
1298G VAL* 4.8 1.9 - - - +
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Residues in contact with GLY1268 (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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1238G ASP* 3.5 17.0 + - - -
1241G ALA* 3.8 13.7 - - - +
1242G TYR* 3.9 13.9 - - - -
1264G ILE* 3.7 11.2 - - - -
1265G SER* 3.0 11.4 + - - -
1267G ALA* 1.3 75.8 - - - +
1269G ILE* 1.3 63.3 + - - +
1271G ARG* 3.4 3.6 + - - +
1272G LEU* 3.2 18.0 + - - +
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Residues in contact with ILE1269 (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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1259G VAL* 4.9 0.2 - - + -
1264G ILE* 3.5 25.8 - - + +
1265G SER 2.9 22.6 + - - +
1266G GLY 3.8 3.4 - - - +
1268G GLY* 1.3 71.7 - - - +
1270G LEU* 1.3 64.9 + - - +
1272G LEU* 3.3 14.7 + - + +
1273G VAL* 3.1 25.4 + - + +
1287G ILE* 3.4 52.0 - - + -
1290G GLN* 4.2 11.0 - - + +
1294G LEU* 3.8 30.1 - - + -
1302G ILE* 3.9 11.7 - - + -
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Residues in contact with LEU1270 (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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1266G GLY 2.8 23.0 + - - +
1267G ALA* 3.5 8.7 - - - +
1268G GLY 3.3 0.2 - - - -
1269G ILE* 1.3 74.8 - - - +
1271G ARG* 1.3 52.1 + - - +
1273G VAL* 3.1 16.1 + - + +
1274G GLU* 2.8 61.7 + - + +
1298G VAL* 4.5 8.9 - - + +
1301G GLU* 3.5 61.0 - - + +
1302G ILE* 4.2 7.0 - - + +
1305G MET* 4.8 0.4 - - + -
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Residues in contact with ARG1271 (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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1242G TYR* 3.6 58.9 + - + +
1245G ALA* 3.4 24.3 - - + +
1246G GLU* 5.5 5.1 + - - +
1267G ALA 3.0 16.5 + - - +
1268G GLY 3.6 5.4 - - - +
1269G ILE 3.3 0.2 - - - -
1270G LEU* 1.3 72.2 - - - +
1272G LEU* 1.3 67.7 + - - +
1274G GLU* 3.3 28.3 + - - +
1275G ALA* 3.4 6.8 + - - +
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Residues in contact with LEU1272 (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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1241G ALA* 3.6 31.2 - - + +
1244G LEU* 3.8 14.8 - - + -
1245G ALA* 3.7 17.5 - - - +
1248G LEU* 4.2 14.3 - - + +
1257G LEU* 4.3 10.3 - - + -
1259G VAL* 4.3 26.5 - - + -
1264G ILE* 5.4 0.2 - - + -
1268G GLY 3.2 14.6 + - - +
1269G ILE* 3.3 19.7 - - + +
1271G ARG* 1.3 79.1 - - - +
1273G VAL* 1.3 58.1 + - - +
1275G ALA* 3.1 24.3 + - - +
1276G LEU 3.9 1.9 + - - -
1285G MET* 4.2 27.9 - - - +
1287G ILE* 4.7 1.3 - - + -
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Residues in contact with VAL1273 (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* 3.1 17.4 + - + +
1270G LEU* 3.1 25.6 - - + +
1272G LEU* 1.3 72.0 - - - +
1274G GLU* 1.3 58.0 + - - +
1275G ALA 3.0 5.4 - - - -
1276G LEU* 2.9 41.6 + - + +
1277G PRO* 3.6 3.8 - - - +
1285G MET* 4.2 19.5 - - - -
1287G ILE* 6.1 1.8 - - + -
1302G ILE* 4.1 26.9 - - + +
1305G MET* 3.7 27.4 - - + +
1306G LEU* 5.0 5.2 - - + -
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Residues in contact with GLU1274 (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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1249G LYS* 4.6 3.7 - - - -
1270G LEU* 2.8 42.3 + - + +
1271G ARG* 3.5 30.9 + - - +
1272G LEU 3.2 0.2 - - - -
1273G VAL* 1.3 77.9 - - - +
1275G ALA* 1.3 59.2 + - - +
1276G LEU 3.3 0.2 - - - -
1277G PRO* 3.5 11.1 - - - +
1278G TYR* 3.8 14.4 - - - -
1305G MET* 4.0 27.2 - - + +
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Residues in contact with ALA1275 (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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1245G ALA* 3.3 30.7 - - + +
1248G LEU* 3.9 15.2 - - + +
1249G LYS* 4.0 18.0 - - + +
1271G ARG 3.4 5.3 + - - +
1272G LEU 3.1 14.2 + - - +
1273G VAL 3.0 1.0 - - - -
1274G GLU* 1.3 78.2 - - - +
1276G LEU* 1.3 58.4 + - - +
1277G PRO 3.3 0.4 - - - -
1278G TYR* 2.8 29.0 + - - +
1279G ASN* 3.5 6.7 + - - +
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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