Contacts of the strand formed by residues 67 - 73 (chain H) 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 PRO 67 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7H ILE* 3.6 33.2 - - + -
58H LEU 4.0 5.6 - - - +
59H THR* 4.0 8.7 - - + -
65H TYR 3.4 9.2 - - - +
66H LYS* 1.3 93.8 - - + +
68H TRP* 1.3 60.8 + - - +
84H LEU* 3.9 21.8 - - + +
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Residues in contact with TRP 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H VAL* 3.6 27.8 - - + -
33H ILE* 3.6 14.6 - - + -
35H ASN* 2.9 41.1 - - + -
36H LYS 4.4 0.2 - - - -
37H PRO* 3.4 30.0 - - + +
38H GLU 4.8 2.9 - - - +
41H ILE* 3.4 17.9 - - + -
58H LEU* 3.0 19.4 + - + +
59H THR* 4.6 2.9 - - - -
66H LYS 4.3 3.6 - - - +
67H PRO* 1.3 78.8 - - - +
69H ALA* 1.3 79.9 + - + +
83H MET* 3.1 30.6 - - + +
84H LEU* 2.9 35.2 + - - +
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Residues in contact with ALA 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H ILE* 4.4 11.9 - - + -
57H LEU* 3.7 1.4 - - - +
58H LEU* 2.7 38.9 + - + +
68H TRP* 1.3 102.3 - - + +
70H LEU* 1.3 60.2 + - - +
81H ILE* 4.7 2.7 - - + -
82H LYS 3.4 13.0 - - - +
83H MET* 3.8 15.3 - - - -
84H LEU* 3.6 8.6 - - - +
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Residues in contact with LEU 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H ILE* 4.5 16.2 - - + -
11H GLU* 3.7 31.4 - - + +
12H THR* 3.7 18.2 - - + -
55H VAL* 4.8 2.9 - - + -
56H MET 3.4 9.4 - - - +
57H LEU* 4.4 15.9 - - + -
69H ALA* 1.3 71.9 - - - +
71H VAL* 1.3 71.6 + - - +
72H ILE* 3.7 33.2 - - + -
80H LYS 3.8 4.3 - - - +
81H ILE* 3.7 1.0 - - - +
82H LYS* 3.0 39.4 + - + +
84H LEU* 3.9 9.3 - - + +
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Residues in contact with VAL 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195G LEU* 4.6 6.7 - - + -
33H ILE* 4.5 11.0 - - + -
54H ASN 3.5 2.6 - - - +
55H VAL* 3.6 1.7 - - - -
56H MET* 2.8 56.5 + - + +
58H LEU* 3.9 19.7 - - + -
69H ALA 4.8 0.7 - - - -
70H LEU* 1.3 82.5 - - - +
72H ILE* 1.3 66.5 + - - +
73H GLN 4.0 0.2 - - - -
79H ASN* 3.5 40.8 - - + +
80H LYS 3.9 5.2 - - - +
81H ILE* 4.3 21.8 - - + -
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Residues in contact with ILE 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H THR* 4.1 16.2 - - + -
53H GLU* 3.3 45.3 - - + +
54H ASN 3.4 2.7 - - - +
55H VAL* 4.4 14.6 - - + -
70H LEU* 3.7 21.3 - - + -
71H VAL* 1.3 78.6 - - - +
73H GLN* 1.3 58.5 + - - +
74H ASP 3.9 0.5 + - - -
78H GLU 3.4 5.4 - - - +
79H ASN* 4.3 1.1 - - - -
80H LYS* 3.3 49.5 + - + +
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Residues in contact with GLN 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G ASN* 5.4 0.3 + - - -
194G PRO* 3.2 33.5 + - - +
195G LEU* 4.6 0.6 - - - +
198G SER* 5.3 4.0 + - - -
53H GLU* 3.4 4.3 - - - -
54H ASN* 2.8 62.4 + - + +
56H MET* 3.6 15.8 - - + +
71H VAL 4.0 1.2 - - - -
72H ILE* 1.3 72.5 - - - +
74H ASP* 1.3 69.0 + - - +
77H GLY* 3.8 15.8 + - - +
78H GLU 3.4 5.8 - - - -
79H ASN* 3.3 29.7 + - - +
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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