Contacts of the strand formed by residues 1318 - 1322 (chain B) in PDB entry 1Y8Z
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 ILE1318 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288B GLY 3.5 1.8 + - - -
1289B PHE* 3.6 20.8 - - + -
1290B GLY 3.1 21.7 + - - +
1317B THR* 1.3 79.0 + - - +
1319B PRO* 1.3 74.6 - - + +
1320B VAL* 3.5 1.8 + - + +
1344B GLY 4.4 4.5 - - - +
1346B ILE* 3.7 32.8 - - + -
1363B LEU* 4.0 6.5 - - + -
1370B TYR* 3.3 41.3 + - + +
1373B GLU* 3.8 13.0 - - + -
1374B ARG* 3.6 33.7 - - + +
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Residues in contact with PRO1319 (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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1290B GLY 3.8 4.0 - - - +
1312B LEU* 4.1 7.6 - - + -
1313B GLY* 3.9 26.0 - - - +
1317B THR 3.2 11.4 - - - +
1318B ILE* 1.3 88.6 - - + +
1320B VAL* 1.3 60.0 + - - +
1321B PHE* 3.5 30.3 - - + -
1344B GLY 4.6 4.3 - - - +
1345B ILE* 3.8 6.7 - - + +
1346B ILE* 3.0 26.5 + - - +
1377B ALA* 3.8 24.7 - - + -
1381B LEU* 4.5 3.4 - - + -
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Residues in contact with VAL1320 (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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1289B PHE* 4.3 8.7 - - + -
1290B GLY 2.9 17.5 + - - +
1291B TYR* 3.6 39.2 - - + -
1292B GLN 3.0 26.2 + - - +
1293B LEU* 3.8 1.8 - - + +
1318B ILE 4.0 6.3 - - - +
1319B PRO* 1.3 75.0 - - - +
1321B PHE* 1.3 62.0 + - - +
1346B ILE* 3.2 32.8 - - + +
1348B PHE* 3.8 24.9 - - + -
1356B THR* 4.6 2.9 - - + -
1360B ILE* 4.6 4.0 - - + -
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Residues in contact with PHE1321 (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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1292B GLN* 3.3 10.5 - - + +
1293B LEU* 4.2 0.9 - - - -
1305B LEU* 4.6 7.6 - - + -
1309B HIS* 3.4 57.4 - + + -
1312B LEU* 3.6 18.2 - - + -
1319B PRO* 3.5 23.7 - - + -
1320B VAL* 1.3 82.3 - - - +
1322B TRP* 1.3 59.6 + - - +
1325B THR* 6.0 0.7 - - + -
1345B ILE* 3.8 33.4 - - + -
1346B ILE 2.9 6.5 + - - -
1347B TRP* 3.5 28.3 - + + -
1348B PHE* 2.6 37.5 + - - +
1381B LEU* 4.4 12.8 - - + -
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Residues in contact with TRP1322 (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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1213B GLN* 3.4 40.2 - - + -
1292B GLN 3.6 5.5 + - - -
1293B LEU* 3.8 26.2 - - + +
1294B SER 3.2 22.6 + - - +
1295B LYS* 3.6 26.0 - - + +
1309B HIS* 5.5 0.4 - - - -
1321B PHE* 1.3 72.4 - - - +
1323B LYS* 1.3 67.8 + - + +
1324B SER* 2.9 34.0 + - - +
1325B THR* 3.0 23.8 + - - +
1326B GLY 3.2 9.0 + - - -
1347B TRP* 3.6 4.4 - - - -
1348B PHE* 3.8 27.6 - + - -
1350B GLU* 3.5 44.6 + - + -
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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