Contacts of the strand formed by residues 78 - 85 (chain N) in PDB entry 1CZA
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 78 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77N LYS* 1.3 78.2 - - - +
79N ASP* 1.3 61.2 + - - +
80N PHE* 3.4 16.7 - - - -
96N GLN* 3.4 2.3 - - - -
97N VAL 2.9 31.4 + - - +
99N HIS* 4.0 15.4 + - - -
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Residues in contact with ASP 79 (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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78N GLY* 1.3 72.5 - - - +
80N PHE* 1.3 64.2 + - - +
94N ARG* 2.6 48.1 + - - +
95N VAL 3.7 2.2 - - - -
96N GLN* 3.3 17.7 - - - +
99N HIS* 3.5 23.3 + - + +
146N LYS* 5.0 2.3 - - - -
148N LEU* 3.5 26.4 - - + +
149N PRO* 3.5 22.2 - - - +
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Residues in contact with PHE 80 (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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77N LYS 3.7 4.0 - - - -
78N GLY* 3.4 33.9 - - - -
79N ASP* 1.3 82.0 + - - +
81N ILE* 1.3 67.7 + - - +
94N ARG* 3.3 7.4 - - - +
95N VAL* 2.8 49.6 + - + +
97N VAL* 4.3 10.3 - - + -
148N LEU* 4.4 2.7 - - - -
149N PRO* 3.6 24.0 - - + +
454N ALA* 4.0 26.7 - - + -
457N THR* 3.5 24.0 - - + -
458N ALA* 3.4 42.0 - - + -
461N TYR* 5.0 4.9 - + + -
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Residues in contact with ILE 81 (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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80N PHE* 1.3 81.0 - - - +
82N ALA* 1.3 66.7 - - - +
83N LEU* 4.7 0.9 - - + -
92N ILE* 4.0 11.4 - - + -
93N LEU 3.3 9.4 - - - +
94N ARG* 5.0 0.7 - - - -
134N LEU* 3.9 20.9 - - + -
137N PHE* 4.8 4.3 - - + -
138N MET* 3.6 31.2 - - + -
143N ILE* 4.3 17.3 - - + +
148N LEU* 3.8 36.1 - - + +
149N PRO 3.0 6.7 + - - +
150N VAL* 3.3 17.7 - - + -
151N GLY 2.8 25.8 + - - +
457N THR* 5.1 0.2 + - - -
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Residues in contact with ALA 82 (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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80N PHE 4.1 0.4 + - - -
81N ILE* 1.3 77.4 - - - +
83N LEU* 1.3 62.4 + - - +
92N ILE* 3.4 3.6 - - - +
93N LEU* 2.8 50.0 + - + +
95N VAL* 4.7 4.9 - - + -
151N GLY* 3.3 7.0 - - - +
450N GLY* 4.0 33.7 - - - +
453N ALA* 4.5 9.4 - - + -
454N ALA* 5.0 4.7 - - + +
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Residues in contact with LEU 83 (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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81N ILE* 4.7 0.2 - - + -
82N ALA* 1.3 75.5 - - - +
84N ASP* 1.3 60.0 + - - +
85N LEU 4.2 0.4 - - - -
90N PHE* 4.6 10.8 - - + -
91N ARG 3.6 2.9 - - - -
92N ILE* 3.6 37.9 - - + -
130N VAL* 4.3 8.3 - - + -
134N LEU* 4.2 20.9 - - + -
150N VAL* 4.1 20.0 - - + -
151N GLY 2.8 11.3 + - - +
152N PHE* 3.7 24.2 - - + -
153N THR* 2.8 28.6 + - - -
189N LEU* 3.7 31.0 - - + -
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Residues in contact with ASP 84 (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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83N LEU* 1.3 75.5 - - - +
85N LEU* 1.3 63.2 + - - +
87N GLY 5.3 1.2 + - - -
89N SER 3.4 7.4 - - - +
90N PHE* 3.3 8.0 - - - -
91N ARG* 2.8 54.9 + - + +
93N LEU* 4.6 9.5 - - + +
153N THR* 3.5 14.3 - - - +
155N SER* 5.6 0.5 + - - -
449N SER* 4.3 3.0 + - - -
450N GLY* 5.1 3.4 + - - +
919N G6P 2.6 54.4 + - - -
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Residues in contact with LEU 85 (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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84N ASP* 1.3 76.2 + - - +
86N GLY* 1.3 58.1 + - - +
87N GLY 3.7 2.0 - - - -
90N PHE* 4.0 33.7 - - + +
114N THR* 5.2 4.5 - - + -
126N LEU* 4.6 10.8 - - + -
127N PHE* 4.9 4.5 - - + -
129N HIS* 6.5 0.2 - - + -
130N VAL* 3.8 26.0 - - + -
152N PHE* 3.9 28.3 - - + -
153N THR 2.9 11.0 + - - +
154N PHE* 3.5 15.1 - - + -
155N SER* 3.1 25.3 + - - -
156N PHE* 4.0 2.0 - - - -
175N PHE* 3.7 34.3 - - + -
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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