Contacts of the helix formed by residues 1236 - 1249 (chain C) in PDB entry 3B13
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 ASN1236 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1201C MET* 4.1 6.1 - - - +
1231C HIS* 2.7 44.6 + - + +
1234C CYS* 3.5 29.1 - - - +
1235C ASP* 1.3 71.1 - - - +
1237C TYR* 1.3 67.0 + - - +
1238C THR 3.4 0.7 - - - -
1239C GLU* 3.2 30.4 - - + +
1240C ALA* 3.3 15.9 + - - +
1366C LYS* 3.9 13.4 + - - +
1480C ARG* 4.4 15.1 - - - +
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Residues in contact with TYR1237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232C LEU* 3.5 28.6 + - + -
1235C ASP* 2.8 41.2 + - + -
1236C ASN* 1.3 72.2 - - - +
1238C THR* 1.3 66.3 + - - +
1240C ALA* 3.2 3.7 + - - +
1241C ALA* 2.9 19.1 + - - +
1287C TYR* 3.4 43.7 - + - +
1290C LYS* 3.6 50.9 + - + +
1291C GLY* 4.2 4.9 - - - +
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Residues in contact with THR1238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1236C ASN 3.4 0.6 - - - -
1237C TYR* 1.3 80.4 - - - +
1239C GLU* 1.3 69.7 + - - +
1241C ALA* 3.3 3.1 + - - +
1242C TYR* 3.0 52.4 + - + -
1287C TYR 4.6 0.4 + - - -
1288C PHE* 3.7 8.9 - - + -
1291C GLY* 3.6 15.4 + - - -
1293C MET* 3.4 26.4 - - + +
1364C ARG* 4.7 6.8 + - - +
1476C PRO* 3.5 22.7 - - + -
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Residues in contact with GLU1239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1231C HIS* 3.5 15.7 - - + +
1236C ASN* 3.2 36.2 - - + +
1237C TYR 3.3 0.2 - - - -
1238C THR* 1.3 86.7 + - - +
1240C ALA* 1.3 59.4 + - - +
1242C TYR* 3.8 1.5 - - - +
1243C THR* 2.8 35.3 + - - +
1364C ARG* 4.4 14.7 + - - -
1476C PRO* 4.5 3.3 - - - +
1477C GLY 3.3 25.4 - - - +
1478C ILE 3.6 13.2 - - - +
1479C LEU 3.9 7.3 - - - +
1480C ARG* 3.7 24.8 - - + +
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Residues in contact with ALA1240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1228C ARG* 4.1 8.0 - - + +
1231C HIS* 3.7 15.6 - - + -
1232C LEU* 3.9 19.3 - - + -
1236C ASN 3.3 19.0 + - - +
1237C TYR 3.2 5.3 + - - +
1238C THR 3.2 0.2 - - - -
1239C GLU* 1.3 75.8 - - - +
1241C ALA* 1.3 65.4 + - - +
1243C THR* 3.0 7.2 + - - -
1244C LEU* 3.0 25.6 + - - +
1287C TYR* 3.7 18.4 - - + -
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Residues in contact with ALA1241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237C TYR 2.9 7.2 + - - +
1238C THR 3.5 2.7 - - - +
1240C ALA* 1.3 75.5 - - - +
1242C TYR* 1.3 64.3 + - - +
1244C LEU* 3.1 4.3 + - - +
1245C LEU* 3.0 25.1 + - - +
1284C ILE* 3.9 10.9 - - + +
1287C TYR* 3.4 29.7 - - + -
1288C PHE* 3.5 39.7 - - + -
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Residues in contact with TYR1242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238C THR* 3.0 34.5 + - + +
1239C GLU 3.9 0.9 - - - +
1240C ALA 3.3 0.2 - - - -
1241C ALA* 1.3 77.1 - - - +
1243C THR* 1.3 61.9 + - - +
1245C LEU* 3.5 24.5 + - + +
1246C LEU* 3.7 4.5 + - - +
1288C PHE* 3.7 19.7 - + - -
1296C GLU* 2.6 31.9 + - - +
1438C TYR* 3.4 23.9 - - - -
1476C PRO* 3.4 33.0 + - + -
1477C GLY* 3.6 36.6 - - - +
1478C ILE* 3.0 14.0 - - + +
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Residues in contact with THR1243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1224C LEU* 3.7 30.4 + - - +
1227C LEU* 3.6 17.5 - - + -
1228C ARG* 3.8 12.8 - - - +
1231C HIS* 3.5 22.2 - - + +
1239C GLU 2.8 27.5 + - - +
1240C ALA 3.0 12.3 + - - -
1241C ALA 3.2 0.2 - - - -
1242C TYR* 1.3 74.2 - - - +
1244C LEU* 1.3 61.0 + - - +
1246C LEU* 2.9 27.0 + - - +
1247C HIS 3.7 0.9 + - - -
1478C ILE* 3.2 21.1 - - + +
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Residues in contact with LEU1244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1224C LEU* 5.1 3.4 - - + +
1225C TYR* 3.8 37.9 - - + +
1228C ARG* 4.2 24.5 - - + +
1240C ALA 3.0 15.7 + - - +
1241C ALA 3.1 1.8 + - - +
1243C THR* 1.3 79.1 + - - +
1245C LEU* 1.3 63.3 + - - +
1247C HIS* 2.9 19.9 + - + +
1248C THR* 3.0 13.9 + - - +
1280C LEU* 4.6 15.5 - - + -
1283C THR* 4.0 16.2 - - + -
1284C ILE* 3.7 23.3 - - + -
1287C TYR* 3.8 24.0 - - + -
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Residues in contact with LEU1245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241C ALA 3.0 19.8 + - - +
1242C TYR* 3.6 23.3 - - + +
1243C THR 3.2 0.4 - - - -
1244C LEU* 1.3 76.9 - - - +
1246C LEU* 1.3 57.2 + - - +
1248C THR* 3.3 13.6 + - - +
1249C TRP* 2.9 31.2 + - - +
1281C TYR* 4.5 5.8 - - + +
1284C ILE* 3.7 18.2 - - + -
1288C PHE* 3.9 27.8 - - + -
1296C GLU* 5.8 2.5 - - - +
1300C LEU* 4.0 25.6 - - + -
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Residues in contact with LEU1246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208C LEU* 4.2 15.0 - - + -
1212C LYS* 6.3 0.9 - - - +
1220C TYR* 3.4 24.4 + - - +
1224C LEU* 3.2 29.6 - - + +
1242C TYR 3.7 1.5 + - - +
1243C THR 2.9 14.9 + - - +
1245C LEU* 1.3 79.5 - - - +
1247C HIS* 1.3 61.5 + - - +
1249C TRP* 3.7 15.1 - - + +
1250C LEU* 4.0 10.7 - - - +
1478C ILE* 3.8 33.4 - - + -
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Residues in contact with HIS1247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221C ILE* 3.8 24.8 - - + +
1224C LEU* 3.5 18.3 - - + +
1225C TYR* 2.9 37.3 + + + +
1244C LEU* 2.9 15.9 + - + +
1246C LEU* 1.3 78.4 - - - +
1248C THR* 1.3 65.5 + - - +
1249C TRP 3.0 1.6 - - - -
1250C LEU* 3.0 23.7 + - + +
1251C LEU* 4.0 7.0 + - + +
1262C VAL* 2.9 27.0 + - + +
1264C GLN* 4.7 6.5 - - + -
1267C GLN* 5.1 1.1 - - - -
1276C LEU* 4.3 11.7 - - + +
1280C LEU* 3.5 20.4 - - + +
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Residues in contact with THR1248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244C LEU 3.0 8.5 + - - +
1245C LEU* 3.3 19.1 + - - +
1247C HIS* 1.3 72.8 - - - +
1249C TRP* 1.3 68.0 + - - +
1250C LEU 2.9 2.0 + - - -
1251C LEU* 2.9 29.1 + - + +
1277C LYS* 3.8 14.9 + - + -
1280C LEU* 3.5 39.7 - - + -
1281C TYR* 3.7 34.3 + - + -
1284C ILE* 4.3 4.0 - - + -
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Residues in contact with TRP1249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1212C LYS* 6.2 1.6 - - - -
1245C LEU 2.9 18.4 + - - +
1246C LEU* 3.7 13.2 - - + +
1247C HIS 3.0 0.6 - - - -
1248C THR* 1.3 78.0 + - - +
1250C LEU* 1.3 70.3 + - + +
1251C LEU 4.3 3.5 - - - +
1277C LYS* 6.0 0.2 - - - -
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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