Contacts of the strand formed by residues 54 - 60 (chain N) in PDB entry 2ZHX
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 ASN 54 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92M ARG* 3.2 30.8 + - - +
96M ASN* 5.2 4.9 + - - +
194M PRO* 3.3 35.6 - - + +
45N THR* 4.7 4.5 - - + -
46N ALA 4.0 4.3 - - - -
47N TYR* 3.5 12.7 - - - -
52N ASP* 5.4 0.5 - - - +
53N GLU* 1.3 69.4 - - - +
55N VAL* 1.3 63.4 + - - +
56N MET* 3.6 6.2 + - + +
71N VAL 3.5 3.1 - - - +
73N GLN* 2.7 51.8 + - + +
74N ASP 6.5 0.4 - - - -
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Residues in contact with VAL 55 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8N ILE* 4.0 37.6 - - + +
12N THR* 5.1 4.7 - - + +
14N LYS* 6.2 1.1 - - + -
16N LEU* 4.0 24.2 - - + -
44N HIS 3.8 0.5 - - - +
45N THR* 3.5 2.3 - - - +
46N ALA* 2.8 44.0 + - + +
48N ASP* 4.7 4.7 - - + +
53N GLU* 3.4 10.2 + - + +
54N ASN* 1.3 72.2 - - - +
56N MET* 1.3 60.8 + - - +
70N LEU* 4.5 16.8 - - + -
71N VAL 3.7 2.7 - - - -
72N ILE* 4.4 20.0 - - + +
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Residues in contact with MET 56 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M PRO* 3.7 11.9 - - + -
195M LEU* 3.4 37.2 - - + +
43N VAL* 4.1 12.6 - - + -
44N HIS 3.1 4.7 - - - +
45N THR* 3.5 28.7 - - + +
54N ASN* 3.7 8.3 - - + +
55N VAL* 1.3 75.6 - - - +
57N LEU* 1.4 59.9 + - - +
58N LEU* 4.1 4.9 + - + -
70N LEU* 3.3 8.9 - - - +
71N VAL* 2.8 60.4 + - + +
73N GLN* 3.5 43.1 - - + +
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Residues in contact with LEU 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N LEU* 5.3 5.8 - - + -
7N ILE* 5.5 9.9 - - + -
8N ILE* 4.5 23.9 - - + +
43N VAL* 4.8 0.2 - - - -
44N HIS* 2.8 48.8 + - + +
55N VAL 4.4 0.2 + - - -
56N MET* 1.4 72.5 - - - +
58N LEU* 1.3 63.2 + - - +
59N THR* 4.5 6.7 - - + -
69N ALA 3.6 6.7 - - - +
70N LEU* 4.6 5.2 - - + +
84N LEU* 6.4 0.7 - - + -
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Residues in contact with LEU 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195M LEU* 3.6 29.2 - - + -
29N VAL* 3.8 21.1 - - + -
33N ILE* 3.8 10.3 - - + -
41N ILE* 3.4 22.4 - - + -
42N LEU 3.3 5.2 - - - -
43N VAL* 4.1 11.7 - - + -
56N MET* 4.5 6.3 - - + +
57N LEU* 1.3 76.3 - - - +
59N THR* 1.3 60.9 + - - +
68N TRP* 3.2 18.8 + - + +
69N ALA* 2.9 36.2 + - + +
71N VAL* 3.4 33.2 - - + -
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Residues in contact with THR 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4N LEU* 4.9 13.5 - - + -
7N ILE* 5.7 4.9 - - + -
41N ILE* 3.2 14.2 - - - +
42N LEU* 3.0 30.2 + - - +
44N HIS* 3.2 29.2 - - + +
57N LEU* 4.4 7.4 - - + +
58N LEU* 1.3 79.4 - - - +
60N SER* 1.3 69.8 + - - +
65N TYR* 4.4 7.7 - - - +
66N LYS 3.4 23.6 + - - +
67N PRO* 4.2 10.8 - - + -
68N TRP* 4.3 2.9 - - - -
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Residues in contact with SER 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39N SER* 6.1 4.0 - - - -
40N ASP 4.1 6.5 - - - -
41N ILE* 4.8 2.7 - - - -
42N LEU* 3.9 5.1 - - - +
59N THR* 1.3 88.4 + - - +
61N ASP* 1.3 70.5 + - - +
64N GLU* 2.5 31.8 + - - +
65N TYR* 4.4 1.4 - - - -
66N LYS* 3.2 25.8 + - - +
68N TRP* 5.0 1.6 - - - +
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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