Contacts of the strand formed by residues 28 - 34 (chain A) in PDB entry 4P8X
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 LYS 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A TYR* 1.3 77.3 - - - +
29A LEU* 1.3 60.1 + - - +
30A VAL* 3.9 10.8 - - + -
57A SER* 3.4 7.6 - - - +
58A HIS* 3.6 23.6 - - + +
205A ASP 5.9 0.2 + - - -
206A PHE* 3.7 39.2 - - + +
260A GLU 5.1 7.2 + - - +
263A VAL* 4.4 10.1 - - + -
355A GLY* 3.0 23.2 + - - +
356A GLY* 3.4 1.6 - - - -
357A ALA 3.0 22.2 + - - -
387A LEU* 4.0 5.8 - - - +
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Residues in contact with LEU 29 (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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27A TYR 3.9 0.9 + - - +
28A LYS* 1.3 74.3 - - - +
30A VAL* 1.3 58.7 + - - +
31A CYS* 3.9 8.3 - - - -
55A LEU 3.5 22.4 - - - +
56A CYS* 3.1 10.5 - - + +
57A SER* 2.7 38.3 + - - +
58A HIS 3.1 3.1 + - - -
357A ALA* 3.3 12.3 - - + +
359A ILE* 3.4 29.4 - - + -
380A VAL* 4.1 17.0 - - + +
383A VAL* 4.2 13.5 - - + -
384A LYS* 4.2 27.1 - - + +
387A LEU* 4.4 7.2 - - + -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 4.6 6.7 - - + -
29A LEU* 1.3 71.3 - - - +
31A CYS* 1.3 57.7 + - - +
32A TYR* 4.8 0.7 - - + -
58A HIS* 3.6 20.9 - - + -
60A ILE* 3.5 28.7 - - + -
206A PHE* 4.4 9.2 - - + -
208A ASN* 3.4 20.6 - - - +
263A VAL* 3.1 37.7 - - + -
357A ALA 2.9 6.4 + - - +
358A MET* 3.1 13.2 - - + +
359A ILE* 2.8 31.4 + - - +
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Residues in contact with CYS 31 (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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29A LEU* 3.9 15.0 - - - -
30A VAL* 1.3 76.9 - - - +
32A TYR* 1.3 63.7 + - - +
33A PHE* 3.8 2.1 + - - -
56A CYS* 2.0 50.3 - - + -
58A HIS 3.0 10.6 + - - +
59A LEU* 3.5 11.8 - - + +
60A ILE* 3.0 23.3 + - - -
359A ILE* 4.1 9.4 - - - -
362A ILE* 3.4 24.5 - - + -
380A VAL* 4.4 0.4 - - - -
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Residues in contact with TYR 32 (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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31A CYS* 1.3 75.5 - - - +
33A PHE* 1.3 59.5 + - - +
60A ILE* 3.4 35.2 - - + -
62A SER* 3.2 18.8 - - - -
63A PHE* 5.0 0.2 - + - -
100A SER* 3.9 6.1 - - - -
141A ASP* 2.5 38.4 + - - -
143A SER* 3.2 6.9 + - - -
183A GLY* 4.1 0.2 - - - -
208A ASN* 3.3 11.3 + - - +
358A MET* 3.8 42.8 - - + -
359A ILE 3.1 10.3 + - - +
360A TRP* 3.5 28.5 - + + -
361A SER* 3.3 3.3 - - - -
362A ILE* 2.9 27.0 + - - +
4B NAG 3.8 18.4 - - + +
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Residues in contact with PHE 33 (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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31A CYS 4.2 5.6 - - - -
32A TYR* 1.3 75.4 - - - +
34A THR* 1.3 73.2 + - - +
46A PHE* 3.9 22.2 - + + -
48A PRO* 3.9 21.1 - - + -
51A ILE* 3.8 24.2 - - + -
59A LEU* 4.1 17.0 - - + -
60A ILE 3.0 26.3 + - - +
61A TYR* 3.8 33.9 - + + -
62A SER* 3.0 28.1 + - - -
81A LEU* 4.4 8.5 - - + -
85A ILE* 6.3 0.4 - - + -
88A LEU* 6.3 0.9 - - + -
97A ILE* 5.4 5.4 - - + -
362A ILE* 3.8 17.9 - - + -
363A ASP* 3.6 9.2 - - - +
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Residues in contact with THR 34 (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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33A PHE* 1.3 93.0 - - - +
35A ASN* 1.3 61.5 + - - +
36A TRP* 3.2 54.1 + - + +
37A SER* 3.3 23.0 + - - -
38A GLN* 5.1 0.5 + - - +
46A PHE* 4.6 3.6 - - - +
48A PRO* 5.6 3.3 - - - +
61A TYR* 5.5 0.7 - - - -
62A SER* 3.3 6.3 - - - -
360A TRP* 4.0 16.6 - - + -
361A SER* 4.2 5.2 - - - +
363A ASP* 2.8 27.8 + - - +
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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