Contacts of the strand formed by residues 1462 - 1475 (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 MET1462 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1447B PRO* 4.2 18.2 - - + -
1448B VAL 4.2 4.9 - - - +
1449B ARG* 4.8 2.9 - - + +
1458B GLU* 3.2 31.6 + - + +
1459B PHE* 3.2 27.2 + - + +
1460B ALA 3.5 0.4 - - - -
1461B SER* 1.3 76.9 - - - +
1463B TRP* 1.3 68.4 + - - +
1464B ILE* 4.4 6.3 - - + -
1493B SER 4.4 0.2 - - - -
1494B PRO* 3.1 27.4 - - - +
1497B ASN* 4.5 8.8 + - - +
33D ILE* 4.2 12.1 - - - -
34D PRO* 3.6 38.1 - - + +
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Residues in contact with TRP1463 (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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1447B PRO* 3.4 5.9 - - - +
1448B VAL* 2.9 47.2 + - + +
1450B ARG* 3.5 32.5 - - + +
1460B ALA 5.2 0.4 + - - -
1461B SER* 3.6 15.4 + - - +
1462B MET* 1.3 73.0 - - - +
1464B ILE* 1.3 65.4 + - - +
1491B THR* 3.6 30.1 - - + -
1492B ILE 3.5 4.9 - - - -
1493B SER* 3.6 30.7 - - - -
1494B PRO* 3.4 25.7 - - + +
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Residues in contact with ILE1464 (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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1445B SER* 3.8 19.1 - - - +
1446B ARG 3.3 15.9 - - - +
1447B PRO* 4.2 1.1 - - + -
1448B VAL* 5.5 0.2 - - - -
1462B MET* 4.4 8.5 - - - -
1463B TRP* 1.3 78.3 - - - +
1465B GLU* 1.3 75.1 + - - +
1466B ARG* 4.0 8.3 - - + +
1491B THR* 3.4 7.7 - - - +
1492B ILE* 2.8 60.0 + - + +
1497B ASN* 2.5 39.0 - - - +
33D ILE* 4.1 29.4 - - + -
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Residues in contact with GLU1465 (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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1444B TYR 3.7 1.4 - - - +
1445B SER* 3.5 0.5 - - - -
1446B ARG* 2.8 71.2 + - + +
1448B VAL* 4.2 9.6 - - + +
1463B TRP 4.2 0.8 - - - -
1464B ILE* 1.3 72.3 - - - +
1466B ARG* 1.3 59.3 + - - +
1467B THR* 4.9 1.9 + - - +
1489B GLN* 2.4 36.3 - - + +
1490B THR 4.0 1.8 - - - -
1491B THR* 4.2 13.2 - - + +
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Residues in contact with ARG1466 (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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1443B HIS* 3.6 42.3 + - + +
1444B TYR 3.3 5.2 - - - +
1445B SER* 2.9 29.3 + - - +
1464B ILE* 3.7 7.9 + - + +
1465B GLU* 1.3 74.1 - - - +
1467B THR* 1.3 63.0 + - - +
1468B SER* 5.0 0.2 - - - +
1489B GLN* 3.2 5.1 - - - -
1490B THR* 2.8 60.1 + - + +
1492B ILE* 4.5 18.3 - - + +
1500B GLU* 3.0 40.2 + - - -
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Residues in contact with THR1467 (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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1443B HIS* 3.3 5.4 - - - -
1444B TYR* 2.9 42.1 + - - +
1446B ARG* 5.7 4.2 - - - -
1465B GLU* 4.9 2.1 + - - +
1466B ARG* 1.3 75.7 + - - +
1468B SER* 1.3 69.4 + - - +
1469B PHE* 3.7 29.5 - - + -
1487B MET* 4.7 10.8 - - + -
1488B SER 3.2 11.7 - - - +
1489B GLN* 4.3 10.8 - - + +
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Residues in contact with SER1468 (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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1441B ARG* 3.8 21.9 + - - -
1442B PHE 3.3 7.0 - - - -
1443B HIS* 3.6 19.7 + - - -
1466B ARG* 5.0 0.2 - - - +
1467B THR* 1.3 73.5 - - - +
1469B PHE* 1.3 61.8 + - - +
1470B VAL* 4.3 1.1 - - - -
1486B HIS* 4.4 1.1 - - - -
1487B MET* 3.2 10.4 - - - +
1488B SER* 2.5 52.8 + - - -
1490B THR* 4.6 9.7 - - - +
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Residues in contact with PHE1469 (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* 4.6 4.5 - - + -
1360B VAL* 4.6 1.1 - - + -
1362B ILE* 4.2 14.1 - - + -
1409B PHE* 3.7 33.4 - + - -
1411B VAL* 3.8 18.8 - - + -
1441B ARG* 3.5 2.6 - - - +
1442B PHE* 2.8 47.9 + - + +
1444B TYR* 3.8 7.2 - - + -
1467B THR* 3.7 32.3 - - + -
1468B SER* 1.3 73.0 - - - +
1470B VAL* 1.3 63.4 + - - +
1471B THR 4.2 0.2 - - - -
1484B VAL* 3.9 23.6 - - + -
1486B HIS 3.4 4.7 - - - -
1487B MET* 2.7 41.5 - - + -
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Residues in contact with VAL1470 (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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1440B GLN* 3.5 18.8 - - + +
1441B ARG* 3.9 35.7 - - + +
1468B SER 5.4 0.9 - - - -
1469B PHE* 1.3 77.3 - - - +
1471B THR* 1.3 67.4 + - - +
1484B VAL* 3.6 2.2 - - - -
1485B VAL* 2.8 32.9 + - + +
1486B HIS* 2.9 33.4 + - + +
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Residues in contact with THR1471 (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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1362B ILE* 3.5 36.8 - - + -
1439B VAL 4.8 0.3 + - - -
1440B GLN* 3.0 36.8 + - - +
1442B PHE* 3.8 14.2 - - + -
1470B VAL* 1.3 81.5 - - - +
1472B ALA* 1.3 60.2 + - - +
1473B TYR 2.4 28.6 + - - -
1475B LEU* 5.4 3.4 - - + +
1482B PHE* 3.9 17.3 - - + +
1483B GLU 3.6 10.1 - - - +
1484B VAL* 4.7 0.9 - - - -
1485B VAL* 4.7 1.6 - - - -
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Residues in contact with ALA1472 (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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1440B GLN* 3.2 11.4 + - - +
1470B VAL 4.2 0.2 + - - -
1471B THR* 1.3 75.2 - - - +
1473B TYR* 1.3 88.4 + - + +
1482B PHE* 4.8 1.9 - - + +
1483B GLU* 3.5 10.1 + - + +
1485B VAL* 3.9 24.8 - - + +
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Residues in contact with TYR1473 (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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1440B GLN* 4.0 4.9 - - - +
1471B THR* 2.4 29.3 + - - -
1472B ALA* 1.3 95.7 - - + +
1474B LYS* 1.3 63.2 + - - +
1475B LEU* 3.9 0.3 + - - +
1478B ILE* 6.2 2.7 - - + -
1482B PHE* 3.5 45.8 - + + +
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Residues in contact with LYS1474 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1416B ASP* 3.2 29.0 + - - -
1418B HIS* 4.7 8.1 + - - -
1438B TYR* 3.5 44.0 + - + +
1439B VAL 3.4 5.8 - - - +
1440B GLN* 3.8 25.3 - - + +
1473B TYR* 1.3 74.3 - - - +
1475B LEU* 1.3 62.4 + - - +
1476B PRO 3.6 10.5 - - - +
1477B GLY* 4.3 1.0 - - - -
1482B PHE* 3.1 19.9 - - - -
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Residues in contact with LEU1475 (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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1342B TYR* 3.6 39.0 + - + +
1362B ILE* 4.2 20.2 - - + +
1364B ARG* 4.2 10.1 - - + +
1437B ASN* 3.7 1.4 - - - -
1438B TYR* 2.7 28.4 + - - -
1439B VAL* 2.8 19.0 + - - +
1442B PHE* 4.2 12.6 - - + -
1471B THR* 5.4 2.5 - - + +
1473B TYR 4.8 1.1 - - - +
1474B LYS* 1.3 73.9 - - - +
1476B PRO* 1.3 60.9 - - + +
1479B LEU 3.8 16.6 - - - +
1480B ARG 3.9 13.2 - - - +
1481B TRP* 4.2 1.1 - - - +
1482B PHE* 3.5 31.4 - - + +
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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