Contacts of the helix formed by residues 1237 - 1249 (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 ASN1237 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1210G ILE* 3.9 31.5 - - - +
1235G ARG 4.7 2.9 + - - +
1236G SER* 1.3 74.2 - - - +
1238G ASP* 1.3 65.4 + - - +
1239G PRO* 3.4 21.3 - - + +
1240G VAL* 3.0 16.2 + - - +
1241G ALA 3.2 8.8 + - - -
1263G PHE* 3.5 21.3 - - + +
1264G ILE* 3.8 9.6 - - - +
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Residues in contact with ASP1238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1237G ASN* 1.3 74.9 - - - +
1239G PRO* 1.3 64.1 - - + +
1241G ALA* 3.0 6.2 + - - +
1242G TYR* 2.7 59.1 + - + -
1263G PHE 4.3 1.3 + - - -
1264G ILE* 3.7 2.1 - - - -
1265G SER* 2.9 49.7 + - - -
1267G ALA* 4.4 1.2 - - - +
1268G GLY* 3.5 15.3 + - - -
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Residues in contact with PRO1239 (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* 4.3 6.7 - - + -
1214G LYS* 4.1 29.5 - - + +
1237G ASN* 3.4 18.6 - - - +
1238G ASP* 1.3 94.0 - - + +
1240G VAL* 1.3 63.1 + - - +
1242G TYR* 3.4 12.8 + - + +
1243G ALA* 3.1 24.1 + - - +
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Residues in contact with VAL1240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1210G ILE* 4.1 17.5 - - + +
1213G LEU* 4.0 30.5 - - + +
1214G LYS* 4.5 6.3 - - + +
1217G ALA* 4.8 0.2 - - - +
1231G ILE* 4.0 18.2 - - + -
1236G SER* 3.8 26.7 - - - +
1237G ASN* 3.0 28.8 + - - +
1239G PRO* 1.3 77.8 - - - +
1241G ALA* 1.3 58.2 + - - +
1243G ALA* 3.4 3.1 + - - +
1244G LEU* 2.9 36.8 + - + +
1264G ILE* 5.8 1.3 - - + -
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Residues in contact with ALA1241 (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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1237G ASN 3.2 4.5 + - - +
1238G ASP 3.0 7.7 + - - +
1240G VAL* 1.3 77.1 - - - +
1242G TYR* 1.3 59.2 + - - +
1244G LEU* 4.3 9.6 - - - -
1245G ALA* 2.8 30.2 + - - +
1264G ILE* 3.6 35.4 - - + +
1268G GLY* 3.8 17.3 - - - +
1272G LEU* 3.6 15.9 - - + +
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Residues in contact with TYR1242 (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* 2.7 42.4 + - + +
1239G PRO* 3.7 10.3 - - + +
1241G ALA* 1.3 72.6 - - - +
1243G ALA* 1.3 62.3 + - - +
1245G ALA* 3.2 8.2 + - - +
1246G GLU* 3.1 30.2 + - - +
1267G ALA* 3.7 23.4 - - - +
1268G GLY* 3.9 14.8 - - - -
1271G ARG* 3.6 62.4 + - + +
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Residues in contact with ALA1243 (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* 4.3 21.5 - - + +
1217G ALA* 3.8 18.1 - - + +
1218G GLU* 4.7 9.6 - - - +
1221G LYS* 4.8 1.9 - - - -
1239G PRO 3.1 14.0 + - - +
1240G VAL 3.7 3.6 - - - +
1242G TYR* 1.3 75.8 - - - +
1244G LEU* 1.3 67.2 + - - +
1246G GLU* 3.2 16.4 + - - +
1247G MET* 3.0 21.3 + - - +
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Residues in contact with LEU1244 (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 5.9 0.2 - - - +
1217G ALA* 3.7 17.7 - - + +
1220G LEU* 4.9 0.2 - - + -
1229G PHE* 3.9 26.0 - - + -
1231G ILE* 4.0 15.3 - - + -
1240G VAL* 2.9 29.8 + - + +
1241G ALA* 3.6 8.1 - - - +
1243G ALA* 1.3 77.2 - - - +
1245G ALA* 1.3 61.5 + - - +
1247G MET* 3.1 26.8 + - + +
1248G LEU* 3.0 26.2 + - - +
1257G LEU* 4.5 9.2 - - + -
1259G VAL* 3.9 28.0 - - + -
1264G ILE* 6.1 0.7 - - + -
1272G LEU* 3.8 13.2 - - + -
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Residues in contact with ALA1245 (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 2.8 17.6 + - - +
1242G TYR 3.3 9.6 - - - +
1243G ALA 3.2 0.2 - - - -
1244G LEU* 1.3 68.7 - - - +
1246G GLU* 1.3 66.9 + - + +
1248G LEU* 3.1 11.2 + - - -
1249G LYS* 3.4 5.3 + - - +
1271G ARG* 3.4 43.3 - - + +
1272G LEU* 3.7 8.2 - - - +
1275G ALA* 3.3 23.7 - - + +
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Residues in contact with GLU1246 (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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1218G GLU* 3.5 12.5 - - - +
1221G LYS* 3.4 26.3 + - - +
1242G TYR* 3.1 17.1 + - - +
1243G ALA* 3.2 10.0 + - - +
1245G ALA* 1.3 75.4 - - - +
1247G MET* 1.3 63.7 + - - +
1249G LYS* 3.1 26.8 + - - +
1250G GLU* 3.7 12.0 + - - +
1271G ARG* 5.5 6.0 + - - +
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Residues in contact with MET1247 (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 3.3 27.1 - - - +
1220G LEU* 3.7 20.9 - - + -
1221G LYS* 3.7 22.0 - - + +
1243G ALA 3.0 11.6 + - - +
1244G LEU* 3.1 41.0 + - + +
1246G GLU* 1.3 77.0 - - - +
1248G LEU* 1.3 72.4 + - + +
1250G GLU* 2.9 4.0 + - - +
1251G ASN* 2.8 49.4 + - - -
1254G LEU* 3.8 23.3 - - + -
1257G LEU* 5.1 2.0 - - + -
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Residues in contact with LEU1248 (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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1244G LEU 3.0 17.2 + - - +
1245G ALA 3.1 7.1 + - - +
1247G MET* 1.3 98.0 - - + +
1249G LYS* 1.3 61.0 + - - +
1250G GLU 3.3 0.7 + - - -
1251G ASN* 3.7 5.0 - - + +
1254G LEU* 4.3 7.0 - - + -
1257G LEU* 4.3 6.3 - - + -
1272G LEU* 4.2 23.6 - - + +
1275G ALA* 3.9 9.2 - - + -
1276G LEU* 5.1 3.8 - - + -
1278G TYR 4.0 1.2 - - - +
1279G ASN* 2.9 46.2 + - + +
1282G LEU* 4.2 26.2 - - + -
1285G MET* 3.8 28.3 - - + -
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Residues in contact with LYS1249 (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 3.7 13.2 - - - +
1246G GLU* 3.1 16.6 + - - +
1247G MET 3.1 0.6 - - - -
1248G LEU* 1.3 78.8 - - - +
1250G GLU* 1.3 59.8 + - + +
1252G LYS* 3.7 10.3 + - - -
1274G GLU 4.6 2.7 - - - -
1275G ALA* 4.0 15.3 - - + +
1278G TYR* 3.7 63.6 + - + +
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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