Contacts of the helix formed by residues 1197 - 1214 (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 LYS1197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1198B ASP* 1.3 69.9 + - - +
1199B ASN* 3.1 9.6 - - - +
1200B ARG* 3.1 22.8 + - + +
1201B MET* 2.9 34.6 + - + +
1230B LEU* 5.0 12.1 - - + -
1234B CYS* 5.0 9.9 - - - -
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Residues in contact with ASP1198 (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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1197B LYS* 1.3 74.8 + - - +
1199B ASN* 1.3 61.8 + - - +
1201B MET* 3.2 3.6 + - - +
1202B SER* 2.3 39.8 + - - +
1363B TYR* 4.8 12.5 + - - +
1378B LEU* 5.7 2.1 - - - +
1381B GLN* 3.0 32.6 + - - +
1481B TRP* 3.5 36.8 - - + -
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Residues in contact with ASN1199 (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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1197B LYS* 3.1 5.1 - - - +
1198B ASP* 1.3 84.9 - - - +
1200B ARG* 1.3 64.1 + - - +
1202B SER* 3.3 6.5 + - - -
1203B CYS* 2.9 25.4 + - - +
1355B PHE* 5.2 13.2 - - + -
1381B GLN* 4.9 11.8 + - - -
1382B PHE* 6.0 1.9 - - - -
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Residues in contact with ARG1200 (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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1197B LYS* 3.1 25.0 + - + +
1199B ASN* 1.3 79.2 - - - +
1201B MET* 1.3 50.4 + - - +
1203B CYS* 3.2 8.0 + - - +
1204B THR* 2.4 42.7 + - - +
1230B LEU* 4.4 13.7 - - + -
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Residues in contact with MET1201 (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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1197B LYS* 2.9 26.2 + - + +
1198B ASP* 3.7 5.4 - - - +
1200B ARG* 1.3 75.0 - - - +
1202B SER* 1.3 60.2 + - - +
1204B THR* 3.2 7.3 + - - -
1205B VAL* 2.9 35.2 + - - +
1227B LEU* 4.4 8.1 - - + -
1230B LEU* 3.9 49.1 - - + +
1231B HIS* 4.0 24.7 - - + -
1234B CYS* 4.2 17.5 - - - -
1236B ASN* 4.4 3.4 - - - +
1479B LEU* 3.9 14.4 - - + -
1481B TRP* 4.2 19.3 - - + -
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Residues in contact with SER1202 (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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1198B ASP* 2.3 28.8 + - - +
1199B ASN* 3.6 5.0 - - - -
1201B MET* 1.3 76.6 - - - +
1203B CYS* 1.3 54.6 + - - +
1205B VAL* 3.4 5.5 + - - +
1206B ASN* 2.5 42.2 + - - +
1355B PHE* 3.8 28.9 - - - -
1479B LEU* 5.3 3.8 - - - -
1481B TRP* 3.7 19.3 + - - -
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Residues in contact with CYS1203 (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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1199B ASN 2.9 17.4 + - - +
1200B ARG* 3.2 9.4 - - - +
1202B SER* 1.3 75.0 - - - +
1204B THR* 1.3 67.9 + - - +
1206B ASN* 3.0 12.1 + - - +
1207B LEU* 2.8 43.4 + - - +
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Residues in contact with THR1204 (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 ARG* 2.4 37.6 + - - +
1201B MET* 3.2 7.8 + - - -
1203B CYS* 1.3 75.9 - - - +
1205B VAL* 1.3 51.3 + - - +
1207B LEU* 3.3 9.2 + - - +
1208B LEU* 2.7 36.1 + - + +
1223B TYR* 3.8 41.6 - - + +
1226B LYS* 4.0 11.9 - - + -
1227B LEU* 4.0 17.3 - - + +
1230B LEU* 3.7 10.2 - - + +
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Residues in contact with VAL1205 (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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1201B MET 2.9 21.5 + - - +
1202B SER* 3.8 4.3 - - - +
1204B THR* 1.3 73.2 - - - +
1206B ASN* 1.3 64.1 + - - +
1208B LEU* 3.5 9.5 - - + +
1209B ASN* 2.8 46.7 + - - +
1227B LEU* 3.7 24.5 - - + -
1478B ILE* 4.9 6.1 - - + -
1479B LEU* 3.8 34.5 - - + -
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Residues in contact with ASN1206 (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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1202B SER* 2.5 39.0 + - - +
1203B CYS* 3.5 9.5 - - - +
1205B VAL* 1.3 79.7 - - - +
1207B LEU* 1.3 66.0 + - + +
1209B ASN* 3.4 8.9 + - - +
1210B PHE* 3.2 22.3 + - - +
1355B PHE* 4.6 15.2 - - - +
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Residues in contact with LEU1207 (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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1203B CYS* 2.8 38.7 + - - +
1204B THR* 3.4 9.4 - - - +
1206B ASN* 1.3 73.7 - - + +
1208B LEU* 1.3 65.8 + - - +
1210B PHE* 3.1 11.2 + - + +
1211B TYR* 3.1 35.8 + - + +
1223B TYR* 3.9 41.7 - - + +
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Residues in contact with LEU1208 (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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1204B THR 2.7 19.4 + - - +
1205B VAL* 3.1 11.4 + - + +
1207B LEU* 1.3 73.6 - - - +
1209B ASN* 1.3 74.7 + - - +
1211B TYR* 3.5 4.0 + - - +
1212B LYS 3.2 5.0 + - - -
1220B TYR* 3.2 53.7 - - + +
1223B TYR* 3.6 44.4 - - + +
1224B LEU* 3.7 14.6 - - + +
1227B LEU* 4.1 18.6 - - + -
1246B LEU* 4.4 13.0 - - + -
1478B ILE* 5.9 1.1 - - + -
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Residues in contact with ASN1209 (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 VAL* 2.8 33.1 + - - +
1206B ASN* 3.6 9.0 - - - +
1208B LEU* 1.3 87.5 - - - +
1210B PHE* 1.3 60.7 + - - +
1212B LYS* 3.0 16.0 + - - +
1213B ASP* 2.3 28.3 + - - +
1220B TYR* 5.8 0.4 - - - -
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Residues in contact with PHE1210 (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 ASN 3.2 9.7 + - - +
1207B LEU* 3.1 13.8 + - + +
1209B ASN* 1.3 79.3 - - - +
1211B TYR* 1.3 90.2 + + - +
1213B ASP* 3.0 16.8 + - + +
1214B ASN* 2.5 54.9 + - + -
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Residues in contact with TYR1211 (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 LEU* 3.1 24.9 + - + +
1208B LEU* 3.7 8.7 - - - +
1209B ASN 3.2 0.2 - - - -
1210B PHE* 1.3 102.7 - + - +
1212B LYS* 1.3 56.0 + - - +
1214B ASN* 2.3 29.5 - - + +
1215B ASN* 4.1 0.2 - - - -
1216B ARG* 3.4 18.6 + - + +
1219B MET* 3.8 40.4 - - + -
1220B TYR* 4.0 18.3 - - + +
1223B TYR* 2.9 48.3 + + - -
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Residues in contact with LYS1212 (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 3.2 4.3 + - - +
1209B ASN* 3.0 14.6 + - - +
1211B TYR* 1.3 81.8 - - - +
1213B ASP* 1.3 64.2 + - - +
1214B ASN 3.9 3.5 - - - -
1215B ASN* 4.2 9.2 + - - +
1220B TYR* 3.7 36.3 - - + +
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Residues in contact with ASP1213 (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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1209B ASN* 2.3 32.5 - - - +
1210B PHE* 3.0 13.7 + - + +
1212B LYS* 1.3 80.2 - - - +
1214B ASN* 1.3 68.2 + - - +
1215B ASN* 3.8 8.7 + - - -
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Residues in contact with ASN1214 (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 PHE* 2.5 57.4 + - + +
1211B TYR* 2.3 27.0 - - + +
1213B ASP* 1.3 82.3 - - - +
1215B ASN* 1.3 53.0 + - - +
1216B ARG* 2.6 16.3 + - + +
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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