Contacts of the strand formed by residues 103 - 112 (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 GLN 103 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96N GLN* 4.8 4.8 - - - +
98N ASN* 3.5 8.7 + - - +
99N HIS* 6.0 3.1 - - - +
100N GLU* 3.0 54.8 + - + +
101N LYS 4.2 2.0 - - - +
102N ASN* 1.3 80.9 - - - +
104N ASN* 1.3 75.9 + - - +
105N VAL 3.9 17.5 - - - +
106N HIS* 3.0 39.2 - - + +
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Residues in contact with ASN 104 (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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96N GLN 3.9 0.5 - - - +
97N VAL* 3.5 0.9 - - - -
98N ASN* 2.6 38.7 + - - +
99N HIS 4.5 0.5 + - - -
102N ASN* 4.8 3.8 + - - -
103N GLN* 1.3 86.7 + - - +
105N VAL* 1.3 64.6 + - + +
219N TYR* 3.7 27.9 - - + +
220N ASP* 5.8 1.6 + - - -
451N LYS* 5.9 0.7 - - - +
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Residues in contact with VAL 105 (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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95N VAL* 3.7 23.6 - - + -
96N GLN 3.2 11.9 - - - +
97N VAL* 4.5 2.0 - - + -
103N GLN* 3.9 9.2 - - - +
104N ASN* 1.3 84.7 + - + +
106N HIS* 1.3 63.6 + - - +
107N MET* 3.9 21.1 - - + -
219N TYR* 3.8 17.3 - - + +
451N LYS* 3.5 34.3 - - + +
455N MET* 4.0 10.1 - - + -
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Residues in contact with HIS 106 (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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94N ARG 3.8 1.1 + - - +
95N VAL* 3.5 2.3 - - - -
96N GLN* 2.8 58.9 + - + +
103N GLN* 3.0 34.3 - - - +
105N VAL* 1.3 70.8 - - - +
107N MET* 1.3 74.3 + - - +
108N GLU* 3.7 24.8 + - + -
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Residues in contact with MET 107 (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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93N LEU* 4.5 12.1 - - + -
94N ARG 3.4 6.7 - - - +
95N VAL* 3.4 27.8 - - + -
105N VAL* 3.9 10.1 - - + -
106N HIS* 1.3 88.1 + - - +
108N GLU* 1.3 65.0 + - - +
109N SER* 6.1 0.2 - - - -
447N SER* 4.0 29.8 - - - +
450N GLY 4.1 0.4 - - - -
451N LYS* 3.2 46.2 - - + +
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Residues in contact with GLU 108 (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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93N LEU* 3.2 6.6 - - - +
94N ARG* 3.0 71.0 + - + +
96N GLN* 5.5 1.6 - - - +
106N HIS* 3.7 21.6 + - + -
107N MET* 1.3 76.0 - - - +
109N SER* 1.3 62.2 + - - +
137N PHE* 4.6 1.3 - - + -
141N ARG* 3.7 30.3 + - - +
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Residues in contact with SER 109 (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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91N ARG* 5.1 11.9 + - - -
92N ILE 3.4 7.0 - - - -
93N LEU* 3.8 22.7 - - - -
107N MET* 6.1 0.2 - - - -
108N GLU* 1.3 79.3 - - - +
110N GLU* 1.3 63.7 + - - +
111N VAL* 6.1 0.4 - - - +
137N PHE* 4.6 1.1 - - - -
141N ARG* 4.2 9.7 + - - +
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Residues in contact with GLU 110 (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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91N ARG* 3.3 5.9 - - - -
92N ILE 3.0 29.7 + - - -
109N SER* 1.3 76.4 - - - +
111N VAL* 1.3 72.3 + - - +
112N TYR* 3.5 41.1 + - + -
136N ASP* 4.0 4.8 - - - +
137N PHE* 4.2 5.6 - - + -
140N LYS* 3.0 30.5 + - - +
141N ARG* 3.0 22.5 + - - +
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Residues in contact with VAL 111 (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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89N SER* 3.9 20.9 - - - +
90N PHE 3.5 10.5 - - - +
91N ARG* 3.9 37.0 - - + +
109N SER* 6.1 0.4 - - - +
110N GLU* 1.3 85.0 - - - +
112N TYR* 1.3 71.3 + - - +
113N ASP* 4.1 1.8 + - - +
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Residues in contact with TYR 112 (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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90N PHE* 2.9 30.5 + + + +
92N ILE* 3.9 29.2 - - + -
110N GLU* 3.5 41.5 - - + -
111N VAL* 1.3 80.9 - - - +
113N ASP* 1.3 66.8 + - - +
114N THR* 3.0 13.2 + - - -
133N CYS* 3.3 55.7 + - + -
136N ASP* 2.9 30.3 + - + -
137N PHE* 3.3 15.3 + + - +
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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