Contacts of the helix formed by residues 1236 - 1249 (chain B) in PDB entry 2YIN
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1201B MET* 4.4 6.3 - - - +
1231B HIS* 2.8 33.3 + - + +
1234B CYS* 3.5 21.6 - - - +
1235B ASP* 1.3 72.7 - - - +
1237B TYR* 1.3 67.5 + - - +
1238B THR 3.3 2.2 - - - -
1239B GLU* 3.1 25.1 - - + +
1240B ALA* 2.9 22.9 + - - +
1366B LYS* 3.3 29.0 + - - +
1480B ARG* 3.8 17.9 + - - +
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Residues in contact with TYR1237 (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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1232B LEU* 3.9 26.0 + - + -
1235B ASP* 3.0 50.5 + - + -
1236B ASN* 1.3 72.8 - - - +
1238B THR* 1.3 60.4 + - + +
1239B GLU* 4.5 0.2 + - - -
1240B ALA* 3.0 6.0 + - - +
1241B ALA* 2.7 30.5 + - - +
1287B TYR* 3.6 32.6 - + - +
1290B LYS* 3.8 42.8 - - + +
1291B GLY* 4.0 7.4 - - - +
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Residues in contact with THR1238 (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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1236B ASN 3.3 0.6 - - - -
1237B TYR* 1.3 76.0 - - - +
1239B GLU* 1.3 71.2 + - - +
1241B ALA* 3.2 8.3 + - - +
1242B TYR* 2.9 35.0 + - - -
1287B TYR 5.0 0.2 - - - -
1288B PHE* 4.4 6.1 - - - -
1291B GLY* 3.6 28.5 - - - +
1293B MET* 3.8 24.2 - - + -
1364B ARG* 4.8 8.9 + - - +
1476B PRO* 3.5 26.3 - - - +
1480B ARG* 5.6 2.5 - - - +
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Residues in contact with GLU1239 (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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1231B HIS* 3.6 20.6 - - + +
1236B ASN* 3.1 33.0 - - + +
1238B THR* 1.3 93.5 + - - +
1240B ALA* 1.3 51.7 + - - +
1242B TYR* 3.2 2.3 + - - +
1243B THR* 2.5 38.7 + - - +
1364B ARG* 4.8 2.4 + - - -
1476B PRO* 4.5 7.6 - - - +
1477B GLY 3.2 24.7 - - - +
1478B ILE 4.1 3.6 - - - +
1479B LEU* 3.9 10.6 - - - +
1480B ARG* 3.3 44.8 + - + +
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Residues in contact with ALA1240 (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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1228B ARG* 4.3 11.2 - - + +
1231B HIS* 3.8 16.4 + - + -
1232B LEU* 4.0 20.6 - - + -
1236B ASN 2.9 19.0 + - - +
1237B TYR 3.3 4.0 - - - +
1239B GLU* 1.3 76.8 - - - +
1241B ALA* 1.3 62.3 + - - +
1243B THR* 3.2 17.8 + - - -
1244B LEU* 3.2 17.5 + - - +
1287B TYR* 3.9 12.6 - - + -
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Residues in contact with ALA1241 (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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1237B TYR 2.7 11.6 + - - +
1238B THR 3.4 8.3 - - - +
1240B ALA* 1.3 73.3 - - - +
1242B TYR* 1.3 62.8 + - - +
1243B THR 3.2 0.5 + - - -
1244B LEU* 3.5 2.5 + - - +
1245B LEU* 3.3 17.0 + - - +
1284B ILE* 3.7 21.3 - - + +
1287B TYR* 3.4 32.9 - - + -
1288B PHE* 3.6 26.0 - - + -
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Residues in contact with TYR1242 (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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1238B THR* 2.9 27.8 + - - +
1239B GLU 3.2 4.2 + - - +
1241B ALA* 1.3 77.4 - - - +
1243B THR* 1.3 63.3 + - - +
1245B LEU* 3.3 31.3 - - + +
1246B LEU* 3.8 9.7 + - - +
1288B PHE* 3.8 26.2 - + - -
1293B MET* 5.2 1.9 - - + -
1296B GLU* 2.8 37.9 + - - +
1438B TYR* 4.5 4.5 - - - -
1476B PRO* 3.6 39.1 + - + +
1477B GLY* 3.7 32.1 - - - +
1478B ILE* 4.1 11.2 - - + +
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Residues in contact with THR1243 (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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1224B LEU* 3.7 26.9 + - - +
1227B LEU* 4.3 8.7 - - + -
1228B ARG* 3.8 10.9 + - - +
1231B HIS* 3.7 22.4 - - + +
1239B GLU 2.5 36.3 - - - +
1240B ALA* 3.6 6.3 + - - +
1241B ALA 3.1 0.2 - - - -
1242B TYR* 1.3 75.8 - - - +
1244B LEU* 1.3 62.8 + - - +
1246B LEU* 2.8 37.5 + - - +
1247B HIS 4.0 0.5 + - - -
1478B ILE* 4.0 20.9 - - + -
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Residues in contact with LEU1244 (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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1224B LEU* 5.6 4.0 - - + -
1225B TYR* 3.6 41.1 - - + +
1228B ARG* 4.2 23.3 - - + +
1240B ALA 3.2 9.9 + - - +
1241B ALA 3.9 3.4 - - - +
1243B THR* 1.3 77.3 + - - +
1245B LEU* 1.3 61.6 + - - +
1246B LEU 2.9 6.8 + - - -
1247B HIS* 2.9 25.1 + - + +
1248B THR* 3.4 6.6 + - - +
1280B LEU* 5.1 10.8 - - + -
1283B THR* 4.8 10.8 - - + -
1284B ILE* 3.7 26.2 - - + -
1287B TYR* 3.6 28.0 - - + +
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Residues in contact with LEU1245 (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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1241B ALA 3.3 12.9 + - - +
1242B TYR* 3.3 37.9 - - + +
1243B THR 3.1 0.6 - - - -
1244B LEU* 1.3 75.9 - - - +
1246B LEU* 1.3 62.9 + - + +
1247B HIS 3.3 0.2 - - - -
1248B THR* 3.2 19.9 + - - +
1249B TRP* 3.1 24.6 + - - +
1281B TYR* 4.6 4.7 - - + +
1284B ILE* 3.8 17.9 - - + +
1288B PHE* 4.5 11.7 - - + -
1296B GLU* 5.8 2.2 - - - +
1300B LEU* 4.4 23.3 - - + -
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Residues in contact with LEU1246 (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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1208B LEU* 4.4 12.1 - - + -
1220B TYR* 3.7 22.3 + - - +
1224B LEU* 3.5 28.5 - - + -
1227B LEU* 5.9 0.2 - - + -
1242B TYR 4.0 8.5 - - - +
1243B THR* 2.8 17.9 + - - +
1245B LEU* 1.3 79.7 - - + +
1247B HIS* 1.3 64.1 - - - +
1249B TRP* 3.4 19.4 - - + +
1250B LEU* 3.8 11.4 - - - +
1478B ILE* 4.3 28.3 - - + -
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Residues in contact with HIS1247 (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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1221B ILE* 3.9 30.0 - - + +
1224B LEU* 3.2 22.3 - - + +
1225B TYR* 2.6 38.5 + + - +
1244B LEU* 2.9 14.0 + - + +
1246B LEU* 1.3 74.5 - - - +
1248B THR* 1.3 60.3 + - - +
1250B LEU* 2.9 34.0 + - + +
1251B LEU* 3.5 14.5 + - + +
1276B LEU* 4.4 19.2 - - + +
1280B LEU* 3.9 17.9 - - + +
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Residues in contact with THR1248 (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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1244B LEU 3.4 5.6 + - - +
1245B LEU* 3.2 21.8 + - - +
1247B HIS* 1.3 70.6 - - - +
1249B TRP* 1.3 63.1 + - - +
1250B LEU 2.9 6.1 - - - -
1251B LEU* 3.0 27.8 + - - +
1277B LYS* 3.5 15.9 + - + -
1280B LEU* 3.8 33.0 - - + -
1281B TYR* 3.9 22.2 + - + -
1284B ILE* 3.8 20.0 - - + -
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Residues in contact with TRP1249 (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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1245B LEU 3.1 10.6 + - - +
1246B LEU* 3.4 19.3 - - + +
1247B HIS 3.1 0.4 - - - -
1248B THR* 1.3 82.0 + - - +
1250B LEU* 1.3 67.0 + - + +
1251B LEU 4.1 3.6 - - - +
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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