Contacts of the strand formed by residues 1422 - 1429 (chain A) in PDB entry 6PUO
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 MET1422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1421A GLY* 1.3 74.6 - - - +
1423A GLU* 1.3 64.1 + - - +
1445A VAL* 3.3 1.8 - - - +
1446A SER* 2.5 56.7 + - - +
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Residues in contact with GLU1423 (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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1420A CYS* 5.9 0.3 - - - -
1421A GLY 3.9 9.9 + - - +
1422A MET* 1.3 79.6 - - - +
1424A VAL* 1.3 65.4 + - - +
1425A TYR 5.0 0.4 - - - +
1426A LYS* 4.0 29.2 - - - +
1443A VAL* 3.8 16.5 - - - +
1444A ALA 3.4 4.5 - - - +
1445A VAL* 3.3 34.4 - - - +
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Residues in contact with VAL1424 (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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1351A MET* 4.6 11.7 - - + -
1423A GLU* 1.3 80.4 - - - +
1425A TYR* 1.3 62.1 + - + +
1444A ALA* 2.7 19.9 + - + +
1446A SER* 3.7 29.4 - - - +
1491A LEU 4.9 2.0 - - - +
1494A LYS* 3.5 38.8 - - + +
1495A ALA* 4.2 8.3 - - + +
1498A GLU* 5.5 10.8 - - + -
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Residues in contact with TYR1425 (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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1423A GLU* 5.0 0.2 - - - +
1424A VAL* 1.3 87.4 - - + +
1426A LYS* 1.3 88.4 + - - +
1427A GLY* 3.9 5.1 - - - -
1428A TYR* 2.6 37.0 + - - +
1429A MET* 5.4 3.8 - - + -
1442A THR* 4.1 13.1 - - + +
1443A VAL* 3.8 0.9 - - - -
1444A ALA* 2.9 36.1 + - + +
1491A LEU* 5.5 11.9 - - + -
1494A LYS* 5.4 8.3 - - + -
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Residues in contact with LYS1426 (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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1313A PHE* 4.3 27.6 - - + -
1423A GLU* 4.0 31.1 - - - +
1425A TYR* 1.3 98.2 - - - +
1427A GLY* 1.3 59.3 + - - +
1442A THR 3.4 8.1 - - - +
1443A VAL* 3.7 33.9 - - + -
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Residues in contact with GLY1427 (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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1313A PHE* 4.2 20.2 - - - +
1314A HIS* 5.2 4.5 - - - -
1425A TYR* 3.6 5.7 - - - -
1426A LYS* 1.3 77.8 - - - +
1428A TYR* 1.3 66.9 + - - -
1429A MET 3.5 0.3 + - - -
1441A GLU* 3.3 8.7 - - - -
1442A THR* 3.2 32.0 + - - +
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Residues in contact with TYR1428 (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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1239A HIS* 3.6 33.3 - - + +
1242A ALA* 4.4 1.4 - - - +
1314A HIS* 5.2 12.5 + - + +
1326A ASN* 3.7 17.4 + - - -
1327A PRO* 5.0 9.0 - - + -
1328A MET* 3.6 26.2 - - + -
1425A TYR* 2.6 27.1 + - - +
1427A GLY* 1.3 71.7 - - - -
1429A MET* 1.3 72.6 + - - +
1430A ASP* 4.4 2.5 + - + -
1434A ASN* 3.1 33.4 + - - +
1439A TRP* 3.6 25.6 - + + -
1440A ILE 3.6 6.5 - - - -
1441A GLU* 3.8 16.5 + - + +
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Residues in contact with MET1429 (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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1349A TYR* 3.6 33.7 - - + +
1425A TYR* 5.4 4.5 - - + -
1428A TYR* 1.3 80.5 - - - +
1430A ASP* 1.3 73.1 + - - +
1431A ASP* 3.7 6.5 + - + +
1434A ASN* 3.5 15.2 + - - -
1440A ILE* 2.9 48.3 + - + +
1442A THR* 3.8 29.8 - - + -
1487A ASN* 4.3 20.6 - - + +
1488A HIS* 5.9 1.1 - - + -
1490A THR* 5.9 1.1 - - - +
1491A LEU* 4.3 18.6 - - + -
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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