Contacts of the strand formed by residues 40 - 44 (chain A) in PDB entry 4ZGY
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 PHE 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 4.1 9.2 - - + -
27A LYS* 3.8 31.2 - - + -
28A ILE* 3.9 18.2 - - + -
38A ASP 3.9 12.3 - - - +
39A ALA* 1.3 74.8 - - - +
41A TYR* 1.3 76.6 + - - +
42A VAL* 3.7 22.9 - - + -
286A LEU* 3.4 3.4 - - - +
287A ALA* 2.9 52.1 + - + -
380A TRP* 3.8 17.7 - + - -
403A PRO* 4.6 2.0 - - - -
404A THR* 3.5 19.3 - - - +
406A TYR* 3.9 17.3 - + + -
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Residues in contact with TYR 41 (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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40A PHE* 1.3 76.5 - - - +
42A VAL* 1.3 66.5 + - - +
284A PHE* 3.9 19.5 - + + -
285A THR 3.5 15.3 - - - -
286A LEU* 3.6 30.2 - - + +
325A SER* 3.0 34.0 + - - -
386A MET* 3.3 21.6 - - + +
390A THR* 3.3 13.9 - - - -
391A VAL* 3.6 25.8 + - + -
403A PRO* 4.1 22.9 - - + -
404A THR 2.9 7.3 + - - -
405A ILE* 3.6 23.9 - - + -
406A TYR* 2.9 28.9 + - - -
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Residues in contact with VAL 42 (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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19A THR 5.7 1.8 - - - +
20A ALA 4.5 16.6 - - - +
23A ILE* 4.4 13.5 - - + -
24A LEU* 3.6 40.6 - - + +
40A PHE* 3.7 12.8 - - + -
41A TYR* 1.3 78.8 - - - +
43A ALA* 1.3 64.0 + - - +
44A ASP* 6.3 0.9 - - + -
283A ALA 3.7 1.6 - - - +
284A PHE* 3.6 1.0 - - - -
285A THR* 2.9 36.2 + - - +
406A TYR* 3.5 10.5 - - + +
408A VAL* 4.4 17.5 - - + -
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Residues in contact with ALA 43 (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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41A TYR 4.1 0.2 - - - -
42A VAL* 1.3 76.6 - - - +
44A ASP* 1.3 60.1 + - - +
45A LEU* 3.8 1.2 + - + -
48A ILE* 6.3 0.4 - - + -
76A ILE* 5.6 0.2 - - + -
283A ALA 3.2 4.0 - - - -
284A PHE* 3.5 45.1 - - + -
405A ILE* 4.1 3.8 - - + +
406A TYR 2.9 7.9 + - - +
407A TYR* 3.4 20.1 - - + -
408A VAL* 2.9 28.1 + - - +
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Residues in contact with ASP 44 (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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19A THR* 4.3 24.5 + - - +
42A VAL* 6.3 0.7 - - + -
43A ALA* 1.3 72.0 - - - +
45A LEU* 1.3 62.8 + - - +
46A GLY* 3.1 11.3 + - - -
47A ASP* 3.2 35.9 + - + +
48A ILE* 3.6 1.5 + - - -
283A ALA* 2.9 25.4 + - - +
408A VAL* 3.0 19.5 - - + +
409A MET* 4.6 2.1 - - - -
410A SER 5.1 1.4 + - - -
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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