Contacts of the strand formed by residues 1424 - 1431 (chain A) in PDB entry 2Y23
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 GLY1424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1393A LYS* 4.5 1.6 - - - -
1394A ASP* 3.5 13.7 - - - -
1422A ASP 3.9 0.4 + - - -
1423A ALA* 1.3 75.1 - - - +
1425A ILE* 1.3 63.1 + - - -
1426A TYR* 3.1 17.6 + - - -
1442A LYS* 4.9 2.2 - - - -
1443A LEU 2.9 31.8 + - - -
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Residues in contact with ILE1425 (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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1392A TYR* 3.9 1.2 - - - +
1393A LYS* 3.6 1.4 - - - -
1394A ASP* 3.0 41.2 + - - +
1395A GLU 4.9 0.5 + - - -
1424A GLY* 1.3 68.5 - - - -
1426A TYR* 1.3 63.5 + - - +
1427A GLU* 4.1 11.2 + - - +
1440A ARG* 3.7 48.0 - - + +
1441A LEU 4.0 5.2 - - - +
1442A LYS* 4.0 31.0 - - + +
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Residues in contact with TYR1426 (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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1364A LEU* 4.1 5.3 - - + +
1376A LEU* 4.0 24.7 - - + -
1391A TRP* 5.6 3.8 - + + -
1392A TYR 3.4 14.6 - - - -
1393A LYS* 3.1 32.4 - - + +
1398A ILE* 4.5 9.2 - - + -
1413A LEU* 5.1 8.3 - - + -
1415A ILE* 4.0 25.2 - - + +
1422A ASP* 2.6 36.6 + - - +
1424A GLY 3.1 27.8 - - - -
1425A ILE* 1.3 73.7 - - - +
1427A GLU* 1.3 63.7 + - - +
1440A ARG* 3.6 2.1 - - - +
1441A LEU* 2.9 42.3 + - + +
1443A LEU* 4.0 19.5 - - + -
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Residues in contact with GLU1427 (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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1364A LEU* 4.2 2.5 - - - -
1391A TRP* 3.6 7.0 - - - +
1392A TYR* 3.1 51.1 + - + -
1395A GLU* 4.7 13.0 + - - +
1425A ILE* 4.9 11.9 - - + +
1426A TYR* 1.3 77.4 - - - +
1428A VAL* 1.3 64.9 + - - +
1429A ILE* 4.3 8.8 - - + +
1438A LYS* 3.4 28.8 - - - +
1439A SER 3.2 13.2 - - - +
1440A ARG* 4.0 18.2 + - + +
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Residues in contact with VAL1428 (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 PHE* 3.7 13.6 - - + -
1364A LEU* 3.8 17.3 - - + -
1378A CYS* 5.3 4.9 - - - -
1389A ILE* 4.0 17.0 - - + -
1390A VAL 3.5 10.1 - - - +
1391A TRP* 3.4 50.5 - - + -
1411A CYS* 5.8 1.3 - - - -
1427A GLU* 1.3 74.3 - - - +
1429A ILE* 1.3 64.8 + - - +
1430A LEU* 3.9 18.4 - - + -
1438A LYS* 3.5 4.3 - - - +
1439A SER 3.0 29.0 + - - +
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Residues in contact with ILE1429 (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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1388A HIS 3.7 4.7 - - - +
1390A VAL* 3.2 29.9 + - + +
1392A TYR* 3.6 37.5 - - + +
1427A GLU* 4.8 10.3 - - - +
1428A VAL* 1.3 78.7 - - - +
1430A LEU* 1.3 75.6 + - - +
1431A LYS* 4.5 8.1 - - + +
1436A LYS* 3.8 28.3 - - - +
1437A ASP 3.8 11.9 - - - +
1438A LYS* 4.4 20.4 - - + +
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Residues in contact with LEU1430 (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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1358A PRO* 3.7 31.9 - - + +
1359A HIS 3.8 11.7 - - - +
1360A PHE* 3.7 32.8 - - + -
1380A VAL* 3.7 30.3 - - + -
1383A ILE* 4.5 10.8 - - + -
1387A THR* 5.0 1.3 - - + -
1388A HIS 3.7 3.4 - - - +
1389A ILE* 4.3 14.8 - - + -
1411A CYS* 6.2 0.4 - - - -
1428A VAL* 3.9 13.2 - - + -
1429A ILE* 1.3 84.1 - - - +
1431A LYS* 1.3 62.2 + - - +
1436A LYS* 3.0 29.6 - - - +
1437A ASP 3.3 8.9 + - - +
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Residues in contact with LYS1431 (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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1358A PRO* 4.2 3.5 - - - +
1386A GLU 4.3 0.9 - - - +
1387A THR* 3.5 6.2 - - - +
1388A HIS* 3.2 51.4 + - + +
1429A ILE* 4.5 8.0 - - + +
1430A LEU* 1.3 71.4 - - - +
1432A ASP* 1.3 79.1 + - - +
1435A GLY 4.0 5.4 - - - -
1436A LYS* 3.2 49.8 - - + +
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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