Contacts of the strand formed by residues 44 - 49 (chain D) in PDB entry 4ZXB
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 ILE 44 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C LEU* 3.8 31.6 - - + -
95C PHE* 3.9 18.0 - - + -
103C TRP* 3.5 77.6 + - + +
104C GLY 5.3 1.0 + - - -
36D LEU* 4.0 18.2 - - + -
37D GLN 3.2 8.3 - - - +
38D GLN* 3.8 14.1 - - + -
42D GLY 3.4 11.2 + - - +
43D THR* 1.3 74.9 - - - +
45D LYS* 1.3 62.1 + - - +
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Residues in contact with LYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ALA 5.7 0.2 - - - -
103C TRP* 4.8 1.6 - - - -
36D LEU* 3.4 1.0 - - - -
37D GLN* 2.9 55.8 + - - +
43D THR 5.3 1.1 - - - +
44D ILE* 1.3 77.0 - - - +
46D ARG* 1.3 70.7 + - - +
47D LEU* 3.6 4.9 + - + +
56D SER 4.9 4.9 - - - -
57D GLY 3.7 20.2 + - - -
58D VAL* 3.9 24.7 - - - +
59D PRO* 4.5 6.3 - - - +
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Residues in contact with ARG 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C GLU 3.8 16.4 + - - -
100C TRP* 3.5 21.3 - - - +
101C ALA* 3.7 32.3 + - - +
103C TRP* 4.4 6.1 - - - +
34D TYR* 3.4 48.1 + - + -
35D TRP 3.7 7.2 - - - +
36D LEU* 4.4 7.4 - - + +
45D LYS* 1.3 81.5 - - - +
47D LEU* 1.3 61.7 + - - +
48D ILE 3.6 10.5 - - - +
49D TYR* 3.9 18.5 - - - +
55D ASP* 2.8 51.5 + - - +
58D VAL* 4.0 2.1 - - - +
476E SER* 4.4 10.3 + - - -
477E TYR* 5.9 1.0 - - - +
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Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D TRP* 2.8 17.5 + - + +
36D LEU 4.7 0.7 - - - -
37D GLN* 3.7 35.0 - - + +
45D LYS* 4.3 8.5 - - + +
46D ARG* 1.3 75.3 - - - +
48D ILE* 1.3 71.5 + - + +
54D LEU* 3.6 3.3 - - - +
55D ASP* 2.9 27.8 + - - +
58D VAL* 3.7 32.6 - - + +
62D PHE* 3.8 27.6 - - + -
73D LEU* 4.2 9.9 - - + -
86D TYR* 3.9 26.7 - - + -
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Residues in contact with ILE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU 4.6 0.9 - - - +
34D TYR* 3.1 9.1 - - - +
35D TRP* 3.0 38.6 + - + -
46D ARG* 3.6 5.4 - - - +
47D LEU* 1.3 87.2 - - + +
49D TYR* 1.3 64.3 + - - +
51D THR* 3.4 34.1 - - - +
52D SER* 3.6 3.8 - - - +
53D SER 3.1 12.3 - - - +
54D LEU* 4.0 12.1 - - + -
55D ASP* 4.0 2.9 - - - -
62D PHE* 4.6 0.4 - - + -
63D SER* 3.6 27.8 - - - +
64D GLY* 3.8 3.4 - - - +
73D LEU* 3.5 30.3 - - + -
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Residues in contact with TYR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU 3.7 0.7 - - - -
34D TYR* 3.6 26.9 - - + -
46D ARG* 3.9 10.5 - - - -
48D ILE* 1.3 73.1 - - - +
50D ALA* 1.3 72.7 + - + +
51D THR 3.2 3.4 + - - -
53D SER* 2.8 53.1 + - - +
54D LEU 3.8 15.3 + - - -
55D ASP* 3.6 24.7 - - - -
474E LYS 4.9 0.2 - - - -
476E SER* 3.3 32.5 - - - -
490E GLU* 3.2 42.9 + - + +
491E PRO* 4.6 6.5 - - + +
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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