Contacts of the strand formed by residues 69 - 77 (chain B) in PDB entry 1ZXN
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 GLY 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B TYR* 3.5 34.4 - - - -
65B ASP 3.0 25.3 + - - -
67B ASP 3.8 0.2 - - - -
68B VAL* 1.3 79.6 - - - +
70B ILE* 1.3 61.2 + - - -
71B ASN* 3.1 14.2 + - - -
273B MET* 5.8 0.2 - - - -
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B TRP* 3.9 22.0 - - + -
63B VAL 3.3 11.7 - - - +
64B TYR* 3.7 13.6 - - + -
68B VAL* 4.2 1.4 + - - +
69B GLY* 1.3 70.8 - - - -
71B ASN* 1.3 60.9 + - - +
241B ARG* 3.8 18.4 - - + -
244B TYR* 5.8 0.9 - - + -
270B TYR* 4.6 3.8 - - + +
273B MET* 3.5 51.5 - - + +
274B TYR* 3.2 45.1 - - + +
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Residues in contact with ASN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B MET 3.7 0.3 - - - +
62B TRP* 3.4 12.4 - - - -
63B VAL* 3.0 29.3 + - - +
65B ASP* 2.8 25.1 + - - +
68B VAL* 4.1 15.1 - - + +
69B GLY 3.1 13.9 + - - +
70B ILE* 1.3 75.9 - - - +
72B TYR* 1.3 61.0 + - - +
73B ARG* 2.9 32.3 + - - +
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLN* 3.5 45.4 + - + +
61B MET* 3.7 23.6 - - - -
62B TRP* 3.5 48.6 - + + -
71B ASN* 1.3 73.7 - - - +
73B ARG* 1.3 59.7 + - - +
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Residues in contact with ARG 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLN* 3.3 8.6 - - - -
61B MET 3.1 29.1 + - - +
63B VAL* 4.0 10.6 - - + +
65B ASP* 2.8 46.2 + - - -
71B ASN* 2.9 24.9 - - - +
72B TYR* 1.3 74.4 - - - +
74B GLU* 1.3 85.0 + - - +
75B VAL* 3.8 9.9 - - + +
233B LYS* 4.3 14.0 - - - +
234B ASP* 2.6 38.9 + - - +
237B ALA* 4.5 4.6 - - - +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B THR* 3.4 30.4 - - + +
59B GLN* 3.6 10.3 - - - +
60B GLN* 4.2 13.7 + - + +
73B ARG* 1.3 100.2 + - - +
75B VAL* 1.3 63.0 + - - +
76B THR* 5.6 0.2 - - - +
234B ASP* 4.4 0.2 - - - +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B VAL 3.5 0.9 - - - +
58B THR* 3.2 5.2 - - - -
59B GLN 2.8 35.9 + - - +
61B MET* 3.8 14.6 - - + +
63B VAL* 3.6 29.4 - - + -
73B ARG* 3.8 19.7 - - - +
74B GLU* 1.3 83.1 - - - +
76B THR* 1.3 66.2 + - - +
77B PHE* 4.1 19.1 + - + -
234B ASP* 3.5 36.6 - - + +
238B LEU* 5.5 2.0 - - + -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 3.8 32.2 - - + +
57B VAL 3.1 12.6 - - - +
58B THR* 3.0 23.2 + - - +
74B GLU* 5.5 0.5 + - - +
75B VAL* 1.3 74.9 - - - +
77B PHE* 1.3 63.7 + - - +
232B ASP* 4.5 6.9 - - - +
234B ASP* 2.8 30.4 + - - +
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 4.0 8.5 - - - -
57B VAL* 3.0 51.2 + - + +
59B GLN* 3.7 15.3 - - + -
61B MET* 3.3 33.4 - - + -
75B VAL* 4.1 16.6 - - + -
76B THR* 1.3 80.2 - - - +
78B VAL* 1.3 72.1 + - - +
79B PRO* 3.7 24.9 - - + -
82B TYR* 4.0 11.4 - + + -
228B MET* 6.0 2.9 - - - -
235B ILE* 4.0 26.2 - - + -
238B LEU* 3.9 22.4 - - + -
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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