Contacts of the helix formed by residues 1278 - 1289 (chain A) in PDB entry 1YW2
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 ASN1278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1124A ASP* 2.8 40.0 + - - +
1128A GLN* 3.6 4.9 - - - +
1277A ALA* 1.3 72.8 - - - +
1279A PRO* 1.3 63.5 - - - +
1280A LEU* 2.7 36.2 + - - +
1281A ALA* 2.6 33.1 + - + +
1282A VAL* 3.2 4.6 + - - +
1307A TYR* 3.2 21.5 - - + -
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Residues in contact with PRO1279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1277A ALA 2.9 12.1 - - - +
1278A ASN* 1.3 85.7 - - - +
1280A LEU* 1.3 64.2 + - + +
1282A VAL* 3.8 9.6 - - + +
1283A ASP* 3.1 24.8 + - - +
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Residues in contact with LEU1280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278A ASN* 2.7 24.0 + - - +
1279A PRO* 1.3 74.0 - - + +
1281A ALA* 1.3 65.3 - - - +
1282A VAL 3.2 0.2 + - - -
1283A ASP* 3.2 9.7 + - + +
1284A LEU* 2.9 23.4 + - - +
1305A HIS* 3.8 7.7 - - + -
1306A ALA* 3.4 37.5 - - + +
1307A TYR* 3.6 24.7 - - + +
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Residues in contact with ALA1281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1213A MET* 4.5 1.8 - - - +
1217A LEU* 3.9 22.0 - - + -
1277A ALA* 5.1 0.7 - - + -
1278A ASN* 2.6 22.2 + - + +
1280A LEU* 1.3 75.2 - - - +
1282A VAL* 1.3 57.2 + - + +
1284A LEU* 3.3 3.4 + - - +
1285A LEU* 2.9 33.8 + - - +
1307A TYR* 3.2 42.7 - - + +
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Residues in contact with VAL1282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217A LEU* 6.1 0.7 - - + -
1270A PHE* 3.6 36.5 - - + -
1271A ALA* 4.1 5.2 - - - +
1274A PHE* 2.8 38.8 - - + +
1277A ALA* 4.3 7.4 - - + +
1278A ASN 3.6 14.1 - - - +
1279A PRO* 3.9 11.9 - - + +
1280A LEU 3.1 0.6 - - - -
1281A ALA* 1.3 76.4 - - + +
1283A ASP* 1.3 56.5 + - - +
1285A LEU* 3.3 9.3 + - + +
1286A GLU* 2.8 35.2 + - - +
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Residues in contact with ASP1283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1279A PRO 3.1 18.8 + - - +
1280A LEU* 3.7 10.4 - - + +
1282A VAL* 1.3 76.2 - - - +
1284A LEU* 1.3 59.4 + - - +
1286A GLU* 3.4 20.5 - - - +
1287A LYS* 2.5 50.7 + - - +
1305A HIS* 3.0 14.0 + - - -
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Residues in contact with LEU1284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1213A MET* 3.6 32.3 - - + -
1280A LEU 2.9 12.9 + - - +
1281A ALA* 3.5 8.3 - - - +
1283A ASP* 1.3 74.5 + - - +
1285A LEU* 1.3 65.7 + - - +
1287A LYS* 2.9 16.6 + - + +
1288A MET* 2.9 41.4 + - + +
1297A ILE* 4.6 7.2 - - + -
1302A ALA* 4.4 15.0 - - + -
1305A HIS* 3.9 33.0 - - + -
1307A TYR* 4.2 7.4 - - + -
1308A PHE* 3.6 22.7 - - + -
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Residues in contact with LEU1285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210A GLY* 3.3 35.2 - - - +
1213A MET* 3.9 16.8 - - + -
1214A ALA* 4.1 7.2 - - + +
1217A LEU* 3.5 30.3 - - + -
1270A PHE* 3.6 12.1 - - + -
1274A PHE* 4.4 19.5 - - + -
1281A ALA 2.9 24.8 + - - +
1282A VAL* 3.5 10.3 - - + +
1284A LEU* 1.3 75.1 - - - +
1286A GLU* 1.3 56.2 + - - +
1288A MET* 2.9 6.0 + - - +
1289A LEU* 2.7 50.4 + - + +
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Residues in contact with GLU1286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267A LYS* 3.3 34.2 + - - +
1268A MET 5.1 0.2 - - - +
1270A PHE* 3.3 45.4 + - + +
1282A VAL* 2.8 21.1 + - - +
1283A ASP* 3.4 15.9 - - - +
1285A LEU* 1.3 72.7 - - - +
1287A LYS* 1.3 62.2 + - + +
1289A LEU 3.9 7.4 - - - +
1290A VAL* 3.7 14.7 - - - +
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Residues in contact with LYS1287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283A ASP* 2.5 45.7 + - - +
1284A LEU* 2.9 12.2 + - + +
1286A GLU* 1.3 80.9 - - + +
1288A MET* 1.3 56.9 + - - +
1290A VAL* 3.7 13.4 - - - +
1295A LYS 4.7 0.5 - - - +
1296A ARG* 3.9 0.3 - - - -
1297A ILE* 3.2 45.4 + - + -
1305A HIS* 3.8 18.2 + - + -
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Residues in contact with MET1288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131A ILE* 5.0 1.8 - - + -
1135A LEU* 3.9 20.0 - - + -
1206A ILE* 3.9 22.2 - - + +
1207A TRP* 4.0 6.1 - - - -
1209A VAL* 3.8 22.7 - - + -
1210A GLY* 4.0 27.1 - - - -
1213A MET* 4.7 8.1 - - - +
1284A LEU* 2.9 42.9 + - + +
1285A LEU* 2.9 6.5 + - - +
1287A LYS* 1.3 78.4 - - - +
1289A LEU* 1.3 65.6 + - - +
1290A VAL 3.2 1.8 + - - -
1296A ARG* 3.1 25.6 + - - +
1297A ILE* 3.9 13.7 - - + -
1302A ALA* 4.0 13.7 - - + -
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Residues in contact with LEU1289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1207A TRP* 3.5 56.8 - - + +
1210A GLY* 3.9 14.1 - - - -
1211A CYS* 3.9 6.1 - - - +
1222A LEU* 3.4 29.8 - - + -
1223A PHE* 4.5 1.1 - - + -
1238A LEU* 4.4 11.9 - - + -
1239A VAL* 3.7 17.0 - - + +
1270A PHE* 4.5 15.6 - - + -
1274A PHE* 5.0 2.0 - - + -
1285A LEU* 2.7 36.9 + - + +
1286A GLU 3.9 7.9 - - - +
1288A MET* 1.3 74.5 - - - +
1290A VAL* 1.3 58.0 + - - +
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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