Contacts of the strand formed by residues 1481 - 1492 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1197A LYS* 4.6 7.4 - - - -
1198A ASP* 3.7 44.9 - - + -
1201A MET* 4.2 17.0 - - + -
1202A SER* 3.4 26.7 + - - -
1361A PHE* 3.8 26.1 - + + -
1362A ILE 3.1 11.9 - - - +
1363A TYR* 3.9 41.8 + + + -
1475A LEU* 4.4 0.7 - - - -
1479A LEU* 3.2 29.1 - - + +
1480A ARG* 1.3 102.9 - - + +
1482A PHE* 1.3 81.8 + - - +
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Residues in contact with PHE1482 (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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1361A PHE* 3.8 5.4 - - - -
1362A ILE 3.0 27.7 + - - -
1471A THR* 3.7 22.5 - - + +
1472A ALA* 4.7 0.7 - - + +
1473A TYR* 3.6 50.9 - + + +
1474A LYS 3.2 19.7 - - - -
1475A LEU* 3.5 29.1 - - + +
1477A GLY* 4.2 4.9 - - - -
1478A ILE* 3.9 29.6 - - + -
1479A LEU* 4.0 21.3 - - + -
1481A TRP* 1.3 83.9 - - - +
1483A GLU* 1.3 67.8 + - - +
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Residues in contact with GLU1483 (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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1355A PHE 5.0 0.2 - - - +
1359A LYS* 3.2 49.2 + - + +
1360A VAL 3.4 11.2 - - - +
1361A PHE* 3.5 24.7 - - + -
1471A THR* 3.5 0.7 - - - -
1472A ALA* 3.3 27.4 + - + +
1482A PHE* 1.3 74.5 - - - +
1484A VAL* 1.3 76.7 + - - +
1485A VAL* 3.5 12.3 + - + +
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Residues in contact with VAL1484 (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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1360A VAL* 2.6 47.4 + - + +
1362A ILE* 3.7 31.9 - - + -
1469A PHE* 3.9 13.2 - - + -
1470A VAL 3.7 7.2 - - - +
1471A THR* 4.3 2.5 - - + +
1482A PHE 3.5 0.2 + - - -
1483A GLU* 1.3 82.9 - - - +
1485A VAL* 1.3 63.7 + - - +
1486A HIS 3.6 22.2 - - - +
1487A MET* 3.7 21.1 - - + -
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Residues in contact with VAL1485 (chain A).
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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1470A VAL* 2.8 13.1 + - + +
1471A THR 4.8 0.2 - - - -
1472A ALA* 4.0 29.8 - - + +
1483A GLU* 3.5 13.7 + - + +
1484A VAL* 1.3 78.3 - - - +
1486A HIS* 1.3 66.1 + - + +
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Residues in contact with HIS1486 (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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1441A ARG* 5.5 4.1 + - - -
1468A SER 3.7 0.5 - - - +
1469A PHE* 3.6 1.2 - - - -
1470A VAL* 3.0 49.4 + - + +
1484A VAL* 3.6 4.9 - - - +
1485A VAL* 1.3 87.8 - - + +
1487A MET* 1.3 82.2 + - - +
1488A SER* 4.4 12.6 + - - -
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Residues in contact with MET1487 (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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1360A VAL* 4.5 19.7 - - - -
1393A ALA* 5.5 11.2 - - + -
1467A THR* 3.8 25.8 - - + -
1468A SER 3.2 8.1 - - - +
1469A PHE* 4.1 17.3 - - + -
1484A VAL* 3.7 14.4 - - + -
1486A HIS* 1.3 93.6 + - - +
1488A SER* 1.3 61.0 + - - +
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Residues in contact with SER1488 (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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1441A ARG* 5.4 3.4 - - - -
1466A ARG 3.9 0.3 - - - +
1467A THR* 3.4 4.9 - - - +
1468A SER* 2.6 51.9 + - - +
1486A HIS* 4.4 14.1 - - - -
1487A MET* 1.3 76.5 - - - +
1489A GLN* 1.3 67.0 + - - +
1490A THR* 4.3 7.3 + - - -
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Residues in contact with GLN1489 (chain A).
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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1465A GLU* 2.8 33.4 - - + +
1466A ARG 3.4 7.6 - - - +
1467A THR* 3.7 18.2 + - + +
1488A SER* 1.3 76.2 + - - +
1490A THR* 1.3 69.4 + - - +
1491A THR* 5.2 3.8 + - - +
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Residues in contact with THR1490 (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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1465A GLU* 3.8 0.9 - - - -
1466A ARG* 2.8 45.4 + - + +
1468A SER* 6.2 0.4 - - - -
1488A SER* 4.2 8.3 + - - -
1489A GLN* 1.3 77.2 + - - +
1491A THR* 1.3 77.1 + - - +
1492A ILE* 5.0 6.7 - - + -
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Residues in contact with THR1491 (chain A).
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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1448A VAL* 6.5 0.7 - - + -
1463A TRP* 3.6 32.6 - - + -
1464A ILE 3.6 11.9 - - - +
1465A GLU* 4.6 11.4 - - + +
1489A GLN* 5.2 2.9 + - - +
1490A THR* 1.3 85.8 + - - +
1492A ILE* 1.3 65.6 + - - +
1496A GLU* 4.3 4.7 - - - +
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Residues in contact with ILE1492 (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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1463A TRP* 3.4 9.0 - - - -
1464A ILE* 2.8 51.3 + - + +
1466A ARG* 4.1 25.4 - - + +
1490A THR* 4.7 5.2 - - + +
1491A THR* 1.3 76.2 - - - +
1493A SER* 1.3 70.7 + - - +
1496A GLU* 3.4 15.9 - - + +
1497A ASN* 3.6 25.8 - - - +
1500A GLU* 3.3 38.8 - - - +
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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