Contacts of the strand formed by residues 90 - 100 (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 PHE 90 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83N LEU* 4.6 6.7 - - + -
84N ASP 3.3 18.4 - - - -
85N LEU* 4.0 30.1 - - + +
89N SER* 1.3 71.5 - - - +
91N ARG* 1.3 72.8 + - - +
92N ILE* 4.1 20.6 - - + -
111N VAL* 3.5 4.4 - - - +
112N TYR* 2.9 47.0 + + + +
114N THR* 3.5 29.1 - - - +
129N HIS* 4.3 5.4 - + - -
130N VAL* 3.9 37.0 - - + -
133N CYS* 3.8 23.6 - - + -
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Residues in contact with ARG 91 (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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82N ALA 3.9 0.2 - - - +
83N LEU 3.5 0.3 - - - -
84N ASP* 2.8 50.5 + - + +
88N SER* 5.4 2.2 + - - -
89N SER* 3.4 25.7 + - - +
90N PHE* 1.3 78.5 - - - +
92N ILE* 1.3 68.3 + - - +
93N LEU* 4.0 20.0 - - + -
109N SER* 5.1 11.3 + - - -
110N GLU 3.3 8.3 - - - +
111N VAL* 3.9 28.8 - - + +
112N TYR* 5.1 0.2 - - - -
919N G6P 4.8 19.2 + - - -
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Residues in contact with ILE 92 (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* 4.0 14.4 - - + -
82N ALA 3.4 8.7 - - - +
83N LEU* 3.6 20.4 - - + -
90N PHE* 4.1 15.7 - - + -
91N ARG* 1.3 78.6 - - - +
93N LEU* 1.3 65.2 + - - +
109N SER* 3.4 2.1 - - - -
110N GLU 3.0 30.0 + - - -
112N TYR* 3.9 14.1 - - + -
133N CYS 3.7 9.0 - - - +
134N LEU* 3.5 36.1 - - + +
137N PHE* 3.4 38.6 - - + -
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Residues in contact with LEU 93 (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* 3.3 9.2 - - - +
82N ALA* 2.8 42.0 + - + +
84N ASP* 4.6 9.2 - - + +
91N ARG* 4.0 24.9 - - + +
92N ILE* 1.3 81.0 - - - +
94N ARG* 1.3 60.9 + - - +
95N VAL* 4.1 13.2 - - + -
107N MET* 4.5 23.6 - - + -
108N GLU 3.2 8.1 - - - +
109N SER* 3.8 20.2 - - - -
137N PHE* 3.7 4.8 - - - -
447N SER 4.7 9.0 - - - +
450N GLY* 4.4 23.6 - - - +
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Residues in contact with ARG 94 (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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79N ASP* 2.6 43.1 + - - +
80N PHE 3.3 7.6 - - - +
81N ILE* 4.6 0.7 - - + +
93N LEU* 1.3 72.8 - - - +
95N VAL* 1.3 60.7 + - - +
96N GLN* 3.7 18.1 + - + +
99N HIS* 5.4 0.2 + - - -
106N HIS* 3.8 1.7 + - - +
107N MET* 3.4 4.0 - - - -
108N GLU* 3.0 62.5 + - + +
137N PHE* 3.7 13.8 - - + -
141N ARG* 4.9 6.3 + - - +
143N ILE* 3.3 41.3 - - + +
146N LYS* 4.4 13.3 - - - +
148N LEU* 3.7 8.1 - - + +
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Residues in contact with VAL 95 (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* 2.8 43.3 + - - +
82N ALA* 4.7 5.4 - - + -
93N LEU* 4.1 18.4 - - + -
94N ARG* 1.3 76.8 - - - +
96N GLN* 1.3 64.2 + - - +
97N VAL* 3.8 7.4 - - + -
105N VAL* 3.7 14.6 - - + -
106N HIS 3.5 2.9 - - - -
107N MET* 3.4 36.1 - - + -
450N GLY 3.9 13.5 - - - +
451N LYS* 4.4 1.8 - - - +
454N ALA* 3.6 25.1 - - + -
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Residues in contact with GLN 96 (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 3.4 4.3 - - - -
79N ASP* 3.3 20.6 - - - +
94N ARG* 3.7 27.6 + - + +
95N VAL* 1.3 73.7 - - - +
97N VAL* 1.3 59.4 + - - +
98N ASN 4.2 0.4 - - - -
99N HIS* 3.1 36.8 + - + +
103N GLN* 4.8 4.8 - - - +
104N ASN 4.5 0.7 - - - -
105N VAL* 3.2 8.7 - - - +
106N HIS* 2.8 69.5 + - + +
108N GLU* 5.5 0.4 - - - -
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Residues in contact with VAL 97 (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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76N GLU* 3.2 31.9 - - + +
77N LYS* 3.1 17.9 - - - +
78N GLY 2.9 21.2 + - - +
80N PHE* 4.3 16.6 - - + -
95N VAL* 3.8 17.5 - - + -
96N GLN* 1.3 78.1 - - - +
98N ASN* 1.3 68.9 + - + +
99N HIS 2.9 2.5 + - - -
104N ASN 3.5 4.7 - - - +
105N VAL* 4.5 3.4 - - + -
219N TYR* 4.9 3.1 - - - +
454N ALA* 4.5 3.1 - - + -
455N MET* 3.7 29.8 - - + -
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Residues in contact with ASN 98 (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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74N GLY* 3.6 15.8 - - - +
76N GLU 3.6 17.5 - - - +
77N LYS* 3.3 26.5 + - + -
97N VAL* 1.3 72.9 - - - +
99N HIS* 1.3 57.0 + - - +
100N GLU 3.2 10.1 + - - +
103N GLN 3.5 7.7 + - - +
104N ASN* 2.6 43.8 + - - +
219N TYR* 3.7 14.9 + - - -
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Residues in contact with HIS 99 (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* 4.8 9.0 + - - +
78N GLY* 4.0 17.6 + - - +
79N ASP* 3.5 24.6 + - + +
94N ARG* 5.4 0.2 + - - -
96N GLN* 3.1 51.1 + - + +
97N VAL 2.9 5.5 + - - +
98N ASN* 1.3 76.1 - - - +
100N GLU* 1.3 60.2 + - + +
103N GLN* 4.6 3.6 + - - +
104N ASN 4.5 0.8 + - - -
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Residues in contact with GLU 100 (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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98N ASN* 3.2 7.9 + - - -
99N HIS* 1.3 81.6 - - + +
101N LYS* 1.3 80.4 + - - +
102N ASN 3.5 0.5 + - - -
103N GLN* 3.0 48.2 + - + +
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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