Contacts of the strand formed by residues 1481 - 1492 (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 TRP1481 (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* 3.5 39.5 - - + -
1201B MET* 4.2 18.4 - - + -
1202B SER* 3.7 24.5 + - - -
1361B PHE* 3.8 24.9 - + + -
1362B ILE 3.0 13.7 - - - +
1363B TYR* 3.7 43.7 + + + -
1475B LEU* 4.5 0.9 - - - -
1479B LEU* 3.1 33.8 - - + +
1480B ARG* 1.3 103.3 - - + +
1482B PHE* 1.3 77.4 + - - +
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Residues in contact with PHE1482 (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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1361B PHE* 3.8 4.9 - - - -
1362B ILE* 3.0 28.4 + - - +
1471B THR* 3.9 23.2 - - + +
1472B ALA* 4.8 0.9 - - + +
1473B TYR* 3.5 50.0 - + + +
1474B LYS 3.1 20.6 - - - -
1475B LEU* 3.5 26.8 - - + +
1477B GLY* 4.3 6.7 - - - -
1478B ILE* 4.0 31.0 - - + -
1479B LEU* 4.0 20.6 - - + -
1481B TRP* 1.3 80.1 - - - +
1483B GLU* 1.3 63.9 + - - +
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Residues in contact with GLU1483 (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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1359B LYS* 3.2 48.3 + - + +
1360B VAL 3.4 12.1 - - - +
1361B PHE* 3.5 24.6 - - + -
1471B THR* 3.6 1.1 - - - -
1472B ALA* 3.5 19.6 + - + +
1482B PHE* 1.3 75.9 - - - +
1484B VAL* 1.3 77.0 + - - +
1485B VAL* 3.4 12.9 + - + +
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Residues in contact with VAL1484 (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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1360B VAL* 2.7 40.6 + - + +
1362B ILE* 3.6 36.3 - - + -
1469B PHE* 3.9 11.4 - - + -
1470B VAL 3.6 7.6 - - - +
1471B THR* 4.3 2.5 - - + +
1483B GLU* 1.3 86.1 - - - +
1485B VAL* 1.3 63.0 + - - +
1486B HIS 3.3 25.6 - - - +
1487B MET* 3.9 19.5 - - + -
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Residues in contact with VAL1485 (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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1470B VAL* 2.8 11.7 + - + +
1471B THR 4.8 0.7 - - - -
1472B ALA* 3.9 30.7 - - + +
1483B GLU* 3.4 14.3 + - + +
1484B VAL* 1.3 78.4 - - - +
1486B HIS* 1.3 63.7 + - + +
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Residues in contact with HIS1486 (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* 5.6 3.7 + - - -
1468B SER* 3.8 0.6 - - - +
1469B PHE* 3.4 1.9 - - - -
1470B VAL* 2.9 49.2 + - + +
1484B VAL* 3.3 5.7 - - - +
1485B VAL* 1.3 86.4 - - + +
1487B MET* 1.3 71.6 + - - +
1488B SER* 3.8 27.7 + - - -
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Residues in contact with MET1487 (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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1348B TYR* 5.1 4.5 - - - +
1360B VAL* 3.9 30.3 - - + -
1409B PHE* 5.4 2.2 - - + -
1467B THR* 4.7 10.5 - - + -
1468B SER 3.2 11.7 - - - +
1469B PHE* 2.7 45.1 - - + -
1484B VAL* 3.9 10.3 - - + -
1486B HIS* 1.3 90.8 + - - +
1488B SER* 1.3 61.3 + - - +
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Residues in contact with SER1488 (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* 4.7 3.6 + - - -
1466B ARG 3.8 0.2 - - - +
1467B THR* 3.2 6.1 - - - +
1468B SER* 2.5 59.7 + - - -
1486B HIS* 3.8 18.1 - - - -
1487B MET* 1.3 75.4 - - - +
1489B GLN* 1.3 59.9 + - - +
1490B THR* 4.9 4.7 - - - +
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Residues in contact with GLN1489 (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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1465B GLU* 2.4 39.2 - - + +
1466B ARG 3.2 12.8 - - - +
1467B THR* 4.7 10.1 - - + +
1488B SER* 1.3 76.8 - - - +
1490B THR* 1.3 68.6 + - - +
1491B THR* 5.1 1.6 - - - +
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Residues in contact with THR1490 (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* 6.3 0.7 - - + -
1465B GLU* 4.0 0.5 - - - -
1466B ARG* 2.8 52.8 + - + +
1468B SER* 4.6 12.6 - - - +
1488B SER* 4.9 3.4 - - - +
1489B GLN* 1.3 78.2 - - - +
1491B THR* 1.3 70.8 + - - +
1492B ILE* 5.2 2.4 - - - +
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Residues in contact with THR1491 (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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1448B VAL* 6.0 2.0 - - + -
1463B TRP* 3.6 34.5 - - + -
1464B ILE 3.4 13.2 - - - +
1465B GLU* 4.2 14.8 - - + +
1489B GLN* 4.8 2.4 + - - +
1490B THR* 1.3 79.7 + - - +
1492B ILE* 1.3 64.0 + - - +
1493B SER 4.2 0.2 + - - -
1496B GLU* 4.1 5.0 - - - +
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Residues in contact with ILE1492 (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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1463B TRP* 3.5 7.2 - - - -
1464B ILE* 2.8 63.7 + - + +
1466B ARG* 4.5 18.4 - - + +
1490B THR* 4.9 2.9 - - - +
1491B THR* 1.3 74.3 - - - +
1493B SER* 1.3 68.0 + - - +
1496B GLU* 3.2 24.7 - - + +
1497B ASN* 3.2 36.9 + - + +
1500B GLU* 3.4 26.0 - - - +
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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