Contacts of the strand formed by residues 1342 - 1347 (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 TYR1342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1340B PRO* 4.2 13.9 - - + -
1341B ASP* 1.3 76.9 + - - +
1343B PHE* 1.3 64.0 + - - +
1362B ILE* 4.1 2.7 - - + -
1363B TYR 3.3 13.2 - - - +
1364B ARG* 3.1 37.7 + - + -
1410B THR* 3.3 7.4 - - - +
1411B VAL* 2.9 48.0 + - + +
1413B PRO* 3.4 32.3 - - + +
1436B SER 2.6 31.1 + - - -
1437B ASN* 4.0 1.4 - - - -
1439B VAL* 3.7 10.6 - - + +
1442B PHE* 3.6 17.5 - + + -
1475B LEU* 3.6 28.3 + - + -
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Residues in contact with PHE1343 (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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1341B ASP* 3.7 20.6 - - + -
1342B TYR* 1.3 79.4 - - - +
1344B ALA* 1.3 64.5 + - - +
1345B VAL 3.7 0.3 + - - -
1361B PHE 3.7 0.5 - - - +
1362B ILE* 3.6 1.0 - - - -
1363B TYR* 2.9 40.0 + - + +
1365B GLY* 3.9 20.6 - - - -
1369B GLU* 3.6 26.2 - - - -
1370B ARG 3.8 1.8 - - - -
1371B ARG* 3.7 33.2 - - + -
1374B PHE* 3.7 52.3 - + + -
1408B CYS* 4.7 4.0 - - - -
1409B PHE 3.3 6.7 - - - +
1410B THR* 3.7 17.3 - - - -
1411B VAL* 4.4 2.9 - - - -
26D ASN* 4.4 1.6 - - - -
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Residues in contact with ALA1344 (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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1343B PHE* 1.3 73.3 - - - +
1345B VAL* 1.3 61.2 + - - +
1360B VAL* 4.4 9.4 - - + -
1361B PHE 3.3 7.0 - - - +
1362B ILE* 3.8 19.7 - - + -
1407B GLN 3.9 0.2 - - - +
1408B CYS* 3.4 4.7 - - - -
1409B PHE* 2.8 49.5 + - + +
1411B VAL* 3.8 20.7 - - + +
1469B PHE* 4.6 2.5 - - + -
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Residues in contact with VAL1345 (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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1343B PHE 4.5 0.9 - - - +
1344B ALA* 1.3 79.6 - - - +
1346B GLY* 1.3 59.5 + - - +
1347B TYR* 3.4 39.9 - - + +
1359B LYS 3.7 1.2 - - - +
1360B VAL* 3.2 5.8 - - - -
1361B PHE* 2.8 37.6 + - + +
1363B TYR* 3.5 23.6 - - + -
1374B PHE* 3.7 29.8 - - + -
1378B LEU* 3.8 16.2 - - + -
1406B ILE* 5.0 0.9 - - + -
1407B GLN 3.1 9.0 - - - +
1408B CYS* 4.1 4.7 - - - -
1409B PHE* 6.1 0.2 - - - -
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Residues in contact with GLY1346 (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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1344B ALA 4.3 0.2 - - - -
1345B VAL* 1.3 73.7 - - - +
1347B TYR* 1.3 61.8 + - - -
1348B TYR* 3.5 27.4 - - - -
1359B LYS 3.4 7.0 - - - -
1360B VAL* 4.3 4.2 - - - +
1405B TYR 3.8 0.2 - - - +
1406B ILE* 3.4 9.4 - - - +
1407B GLN* 2.7 36.6 + - - +
1409B PHE* 5.8 1.2 - - - -
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Residues in contact with TYR1347 (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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1345B VAL* 3.4 28.0 - - + +
1346B GLY* 1.3 71.2 - - - -
1348B TYR* 1.3 56.6 + - - +
1352B PHE* 3.5 39.5 - + + -
1356B LEU* 3.4 35.1 - - + +
1358B ASN* 2.7 36.2 + - - -
1359B LYS 3.0 17.2 + - - -
1361B PHE* 3.8 21.3 - + - -
1363B TYR* 3.1 21.5 + - - -
1378B LEU* 3.7 14.8 - - + +
1381B GLN* 5.5 0.7 + - - -
1382B PHE* 3.7 25.8 - + - -
1405B TYR 3.8 0.9 - - - -
1406B ILE* 4.1 13.0 - - + -
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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