Contacts of the helix formed by residues 1209 - 1221 (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 PRO1209 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1183G VAL* 6.1 0.7 - - + -
1184G GLU* 5.7 3.1 - - - +
1207G ASN 3.4 9.2 - - - +
1208G ILE* 1.3 87.1 - - + +
1210G ILE* 1.3 65.6 + - - +
1211G PRO* 3.2 15.3 - - + -
1212G THR* 2.9 36.3 + - + +
1213G LEU* 3.1 10.7 + - - +
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Residues in contact with ILE1210 (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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1208G ILE 3.4 3.1 + - - +
1209G PRO* 1.3 71.9 - - - +
1211G PRO* 1.3 65.8 - - + +
1213G LEU* 3.3 14.4 + - + +
1214G LYS* 3.0 40.7 + - + +
1234G THR 5.6 0.4 - - - +
1235G ARG 3.9 22.4 - - - +
1236G SER* 4.4 0.2 - - - -
1237G ASN* 3.9 33.4 - - - +
1239G PRO* 4.3 7.9 - - + -
1240G VAL* 4.1 15.7 - - + -
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Residues in contact with PRO1211 (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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1209G PRO* 3.3 13.5 - - + -
1210G ILE* 1.3 95.5 - - + +
1212G THR* 1.3 55.1 + - - +
1214G LYS* 3.8 15.3 - - + +
1215G ALA* 3.0 28.1 + - - +
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Residues in contact with THR1212 (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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1183G VAL* 3.7 29.8 - - + -
1184G GLU* 4.5 11.0 + - - +
1187G LEU* 4.8 9.0 - - + -
1208G ILE* 3.8 9.9 - - + -
1209G PRO* 2.9 30.8 + - + +
1211G PRO* 1.3 75.1 - - - +
1213G LEU* 1.3 66.9 + - - +
1215G ALA* 3.2 7.5 + - - +
1216G TYR* 3.0 35.8 + - + -
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Residues in contact with LEU1213 (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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1202G LEU* 4.6 7.2 - - + -
1208G ILE* 3.6 39.9 - - + +
1209G PRO 3.1 12.9 + - - +
1210G ILE* 3.3 21.3 + - + +
1212G THR* 1.3 77.1 - - - +
1214G LYS* 1.3 62.0 + - - +
1216G TYR* 3.1 18.3 + - + +
1217G ALA* 3.2 12.0 + - - +
1229G PHE* 5.5 2.8 - - + -
1231G ILE* 4.1 25.4 - - + -
1234G THR* 4.3 13.2 - - - +
1236G SER* 3.4 25.6 - - - +
1240G VAL* 4.0 18.7 - - + +
1244G LEU* 5.9 0.3 - - - +
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Residues in contact with LYS1214 (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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1210G ILE* 3.0 36.6 + - + +
1211G PRO* 3.8 13.9 - - + +
1213G LEU* 1.3 75.2 - - - +
1215G ALA* 1.3 57.1 + - - +
1217G ALA* 3.1 6.0 + - - +
1218G GLU* 3.1 33.0 + - + +
1239G PRO* 4.1 35.6 - - + +
1240G VAL* 4.5 3.4 - - - +
1243G ALA* 4.3 15.2 - - + +
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Residues in contact with ALA1215 (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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1187G LEU* 3.8 21.8 - - + +
1191G LYS* 5.8 5.4 - - - +
1211G PRO 3.0 15.7 + - - +
1212G THR* 3.3 11.7 - - - +
1214G LYS* 1.3 74.1 - - - +
1216G TYR* 1.3 66.1 + - - +
1218G GLU* 3.2 9.8 + - - +
1219G ALA* 2.9 25.8 + - - +
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Residues in contact with TYR1216 (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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1183G VAL* 2.5 48.2 + - + +
1186G THR* 3.4 10.4 - - + +
1187G LEU* 3.4 30.3 + - + -
1190G ILE* 3.6 31.1 - - + +
1200G VAL* 4.1 8.3 - - + -
1202G LEU* 3.6 22.8 - - + +
1208G ILE* 5.6 0.4 - - + -
1212G THR* 3.0 32.7 + - + -
1213G LEU* 3.1 13.9 + - + +
1215G ALA* 1.3 75.4 - - - +
1217G ALA* 1.3 63.3 + - - +
1219G ALA* 3.4 2.3 + - - +
1220G LEU* 3.1 29.9 + - - +
1229G PHE* 3.7 28.7 - + + -
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Residues in contact with ALA1217 (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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1213G LEU 3.2 6.2 + - - +
1214G LYS* 3.1 9.8 + - - +
1215G ALA 3.1 0.6 - - - -
1216G TYR* 1.3 79.4 - - - +
1218G GLU* 1.3 64.0 + - - +
1220G LEU* 3.4 6.9 + - - -
1221G LYS* 3.5 1.8 + - - +
1240G VAL* 4.8 0.7 - - + +
1243G ALA* 3.8 12.1 - - + -
1244G LEU* 3.7 50.9 - - + +
1247G MET* 3.3 27.7 - - - +
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Residues in contact with GLU1218 (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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1214G LYS* 3.1 20.7 + - + +
1215G ALA* 3.6 10.8 - - - +
1217G ALA* 1.3 75.0 - - + +
1219G ALA* 1.3 63.9 + - - +
1221G LYS* 3.0 55.9 + - - +
1222G GLU* 4.4 1.6 + - - +
1243G ALA* 4.7 8.4 - - + +
1246G GLU* 3.5 12.0 - - - +
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Residues in contact with ALA1219 (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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1187G LEU* 4.2 6.1 - - + -
1190G ILE* 3.6 22.8 - - + +
1191G LYS* 3.8 32.0 - - + +
1215G ALA 2.9 16.5 + - - +
1216G TYR 3.8 2.9 - - - +
1218G GLU* 1.3 76.7 - - - +
1220G LEU* 1.3 62.6 + - - +
1221G LYS 3.2 0.7 + - - -
1222G GLU* 3.4 5.5 + - - +
1223G ASN* 3.4 17.8 + - - +
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Residues in contact with LEU1220 (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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1190G ILE* 3.8 23.1 - - + -
1216G TYR 3.1 22.5 + - - +
1217G ALA* 3.8 4.0 - - - +
1218G GLU 3.2 0.6 - - - -
1219G ALA* 1.3 74.8 - - - +
1221G LYS* 1.3 66.8 + - - +
1222G GLU 3.2 0.6 + - - -
1223G ASN* 3.4 10.5 + - + +
1226G VAL* 3.9 32.5 - - + -
1229G PHE* 3.7 42.4 - - + -
1247G MET* 3.7 27.8 - - + -
1251G ASN* 2.8 30.1 + - - +
1254G LEU* 5.1 5.4 - - + -
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Residues in contact with LYS1221 (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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1217G ALA 3.5 8.2 + - - +
1218G GLU* 3.0 46.5 + - - +
1219G ALA 3.1 0.8 - - - -
1220G LEU* 1.3 80.2 - - - +
1222G GLU* 1.3 66.1 + - - +
1223G ASN 4.9 0.3 - - - +
1243G ALA 4.8 1.8 - - - -
1246G GLU* 3.4 36.4 + - - +
1247G MET* 3.8 21.3 - - - +
1250G GLU* 3.2 47.2 + - - +
1251G ASN* 3.8 18.7 + - - -
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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