Contacts of the helix formed by residues 1206 - 1219 (chain B) in PDB entry 5JPM
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 PRO1206 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1176B ASN* 5.9 3.1 - - + +
1204B LYS 4.4 1.1 - - - +
1205B ALA* 1.3 90.5 - - + +
1207B VAL* 1.3 56.5 + - + +
1208B ASP* 3.2 7.0 + - + +
1209B LEU* 3.2 29.1 + - + +
1210B LEU* 2.7 32.1 + - - +
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Residues in contact with VAL1207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1205B ALA 5.2 1.8 - - - +
1206B PRO* 1.3 74.8 - - + +
1208B ASP* 1.3 62.0 + - + +
1210B LEU* 3.9 16.0 - - + +
1211B GLY* 2.9 25.6 + - - -
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Residues in contact with ASP1208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1206B PRO* 3.2 5.2 - - + +
1207B VAL* 1.3 85.9 - - + +
1209B LEU* 1.3 65.0 + - + +
1211B GLY* 4.1 0.3 - - - -
1212B VAL* 3.1 31.8 + - - +
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Residues in contact with LEU1209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176B ASN* 4.2 12.6 - - + +
1177B SER* 5.3 3.1 - - - -
1180B GLY* 3.7 39.3 - - - +
1184B SER* 5.3 3.6 - - - -
1200B LEU* 3.9 17.9 - - + +
1205B ALA* 4.8 1.8 - - + -
1206B PRO* 3.2 31.3 + - + +
1208B ASP* 1.3 82.5 - - + +
1210B LEU* 1.3 66.9 + - - +
1212B VAL* 3.5 12.1 - - + +
1213B ALA* 3.1 27.7 + - - +
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Residues in contact with LEU1210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1200B LEU* 3.9 26.7 - - - +
1201B SER* 4.8 13.7 - - - +
1203B THR 5.5 0.2 - - - +
1204B LYS* 5.6 6.3 - - + -
1205B ALA* 4.1 14.9 - - - +
1206B PRO 2.7 22.3 + - - +
1207B VAL* 3.9 15.5 - - + +
1209B LEU* 1.3 73.7 - - - +
1211B GLY* 1.3 64.2 + - - +
1213B ALA* 4.3 3.1 - - - +
1214B HIS* 3.6 18.0 + - - +
1271B HIS* 4.8 3.5 - - - -
1275B HIS* 3.5 34.2 + - + +
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Residues in contact with GLY1211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1207B VAL 2.9 16.8 + - - -
1208B ASP 4.1 0.2 - - - -
1210B LEU* 1.3 81.0 - - - +
1212B VAL* 1.3 59.7 + - - +
1213B ALA 3.2 0.2 - - - -
1214B HIS* 3.2 7.0 + - - +
1215B ASN* 3.0 38.2 + - - +
1275B HIS* 5.1 3.6 - - - -
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Residues in contact with VAL1212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183B ALA* 5.0 5.4 - - + +
1184B SER* 4.7 28.9 - - - +
1208B ASP* 3.1 24.4 + - - +
1209B LEU* 3.5 21.8 - - + +
1211B GLY* 1.3 76.8 - - - +
1213B ALA* 1.3 61.3 + - + +
1215B ASN* 4.4 9.9 - - + +
1216B ASN* 2.8 30.6 + - + +
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Residues in contact with ALA1213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183B ALA* 4.6 15.0 - - + -
1193B ALA* 5.2 2.0 - - - +
1196B THR* 5.1 2.5 - - + -
1197B ALA* 4.5 22.4 - - - +
1200B LEU* 4.2 17.5 - - + -
1209B LEU 3.1 18.7 + - - +
1210B LEU 4.3 3.4 - - - +
1212B VAL* 1.3 77.7 - - - +
1214B HIS* 1.3 59.1 + - - +
1216B ASN* 3.4 6.2 + - - +
1217B LEU* 3.0 28.9 + - - +
1271B HIS* 5.9 0.7 - - + -
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Residues in contact with HIS1214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210B LEU 3.6 11.8 + - - +
1211B GLY* 3.2 8.2 + - - +
1213B ALA* 1.3 75.9 - - - +
1215B ASN* 1.3 73.4 + - - +
1217B LEU* 3.2 4.0 + - - +
1218B MET* 2.9 69.3 + - + +
1271B HIS* 3.1 35.1 + - + +
1272B LEU* 4.4 8.3 - - + -
1275B HIS* 3.8 32.5 + + + +
1276B GLU* 5.7 6.5 + - + -
1281B MET* 5.4 5.5 - - - -
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Residues in contact with ASN1215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1211B GLY* 3.0 23.7 + - - +
1212B VAL* 3.9 9.4 - - + +
1214B HIS* 1.3 91.0 - - - +
1216B ASN* 1.3 62.1 + - - +
1218B MET* 3.6 4.9 + - - +
1219B ALA* 3.3 22.0 + - - +
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Residues in contact with ASN1216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183B ALA* 4.3 19.1 + - - +
1186B GLY* 4.6 14.1 - - - -
1187B LEU 5.2 0.6 - - - +
1188B LEU* 4.9 9.9 - - - +
1193B ALA* 4.0 12.5 - - - +
1212B VAL* 2.8 21.2 + - + +
1213B ALA* 3.7 6.9 - - - +
1214B HIS 3.2 0.2 - - - -
1215B ASN* 1.3 77.9 - - - +
1217B LEU* 1.3 59.7 + - - +
1219B ALA* 3.6 12.7 + - - +
1220B MET* 3.7 35.3 - - - +
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Residues in contact with LEU1217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190B ALA 4.3 2.2 - - - +
1193B ALA* 4.0 15.7 - - + +
1194B ALA* 3.8 31.6 - - + +
1197B ALA* 3.8 22.7 - - + -
1213B ALA 3.0 17.4 + - - +
1214B HIS* 3.2 4.5 + - - +
1216B ASN* 1.3 76.9 + - - +
1218B MET* 1.3 81.8 + - + +
1220B MET* 3.1 12.2 + - + -
1230B TRP* 3.0 49.8 + - + +
1268B ALA* 3.9 20.9 - - + -
1271B HIS* 4.0 6.5 - - + -
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Residues in contact with MET1218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1214B HIS* 2.9 52.6 + - + +
1215B ASN* 4.1 5.8 - - - +
1217B LEU* 1.3 90.9 - - + +
1219B ALA* 1.3 60.5 + - - +
1220B MET 3.4 0.5 + - - -
1221B ALA* 3.4 20.2 + - - +
1228B LEU* 5.4 0.7 - - - -
1230B TRP* 3.8 24.9 - - + -
1272B LEU* 3.6 28.3 - - + -
1281B MET* 4.1 28.3 - - + +
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Residues in contact with ALA1219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B ASN 3.3 16.6 + - - +
1216B ASN* 3.8 10.1 - - - +
1217B LEU 3.1 1.0 - - - -
1218B MET* 1.3 75.6 - - - +
1220B MET* 1.3 62.5 + - + +
1221B ALA 3.4 2.8 + - - +
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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