Contacts of the strand formed by residues 1388 - 1393 (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 HIS1388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1386A GLU* 3.2 20.9 + - - +
1387A THR* 1.3 72.2 - - - +
1389A ILE* 1.3 60.0 + - - +
1390A VAL* 4.2 13.6 - - + +
1400A VAL* 6.3 3.6 - - + -
1401A ASP 5.6 0.7 - - - -
1429A ILE 3.7 4.5 - - - +
1430A LEU* 3.7 1.7 - - - -
1431A LYS* 3.2 48.6 + - + +
1432A ASP* 6.0 1.3 - - - -
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Residues in contact with ILE1389 (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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1380A VAL* 5.6 1.8 - - + -
1383A ILE* 4.6 26.9 - - + -
1387A THR* 3.6 17.1 + - + +
1388A HIS* 1.3 77.1 - - - +
1390A VAL* 1.3 65.8 + - - +
1391A TRP* 4.5 3.4 - - - +
1400A VAL* 3.9 3.7 - - - +
1401A ASP* 3.0 63.0 + - + +
1402A GLU* 6.2 0.7 - - - -
1404A HIS 6.0 1.6 - - - +
1411A CYS* 4.3 21.5 - - - -
1428A VAL* 4.0 20.2 - - + -
1429A ILE 3.7 2.5 - - - -
1430A LEU* 4.3 14.1 - - + -
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Residues in contact with VAL1390 (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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1388A HIS* 4.6 12.6 - - + -
1389A ILE* 1.3 87.0 - - - +
1391A TRP* 1.3 71.9 + - - +
1392A TYR* 3.4 36.8 - - + +
1397A GLU* 4.0 26.2 - - + +
1399A SER 3.8 3.4 - - - +
1400A VAL* 4.7 9.6 - - + -
1427A GLU 3.8 0.5 - - - +
1428A VAL* 3.5 5.1 - - - -
1429A ILE* 3.2 34.1 + - + +
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Residues in contact with TRP1391 (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* 3.9 20.4 - - + -
1376A LEU* 4.2 15.9 - - + -
1378A CYS* 5.0 0.4 - - - -
1389A ILE* 4.5 1.4 - - - +
1390A VAL* 1.3 81.5 - - - +
1392A TYR* 1.3 71.1 + - - +
1397A GLU* 3.5 4.0 - - - -
1398A ILE* 3.1 23.2 + - + -
1399A SER* 3.1 33.0 + - - +
1401A ASP* 3.8 24.3 + - + +
1411A CYS* 4.1 19.5 - - + -
1412A THR* 3.7 24.1 + - - -
1413A LEU* 3.6 56.0 - - + +
1426A TYR* 5.6 4.0 - + + -
1427A GLU 3.6 8.1 - - - -
1428A VAL* 3.4 36.8 - - + +
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Residues in contact with TYR1392 (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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1390A VAL* 3.4 31.9 - - + +
1391A TRP* 1.3 75.2 - - - +
1393A LYS* 1.3 61.5 + - - +
1394A ASP 4.2 0.4 - - - +
1395A GLU* 4.2 12.8 - - - +
1396A ARG 3.4 14.8 - - - +
1397A GLU* 3.4 35.7 + - + -
1398A ILE* 3.5 4.9 - - - -
1425A ILE 4.4 0.9 - - - +
1426A TYR* 3.4 12.3 - - - -
1427A GLU* 3.1 49.9 + - + +
1429A ILE* 3.6 37.0 - - + +
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Residues in contact with LYS1393 (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* 1.3 74.8 - - - +
1394A ASP* 1.3 95.3 + - - +
1396A ARG* 3.1 22.0 + - - +
1398A ILE* 3.4 18.9 - - + +
1421A LYS 2.9 28.3 + - - -
1422A ASP* 4.3 1.8 - - - +
1423A ALA 3.8 11.8 + - - +
1424A GLY* 4.5 1.6 - - - -
1425A ILE 3.6 2.5 - - - +
1426A TYR* 3.1 41.5 - - + +
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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