Contacts of the strand formed by residues 106 - 113 (chain A) in PDB entry 1ZN8
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A SER* 3.5 9.4 + - - -
103A LEU 3.0 27.7 + - - -
104A GLU 3.5 0.2 - - - -
105A TYR* 1.3 80.0 - - - +
107A LYS* 1.3 66.2 + - - +
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Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A SER* 3.8 22.7 - - - +
101A TYR 3.4 8.1 - - - +
102A SER* 5.2 2.0 - - - -
103A LEU* 5.0 1.1 - - - -
106A GLY* 1.3 78.5 - - - +
108A ALA* 1.3 60.7 + - - +
109A GLU* 6.1 0.4 - - + -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LYS* 6.1 1.1 - - + +
100A SER* 3.3 5.0 + - - -
101A TYR* 3.0 59.0 + - + +
103A LEU* 4.2 13.3 - - + +
106A GLY 4.3 0.4 + - - -
107A LYS* 1.3 73.9 - - - +
109A GLU* 1.3 65.4 + - - +
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Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LYS* 3.6 7.4 - - - +
89A ARG* 3.0 65.5 + - + +
98A TRP* 3.7 16.4 + - + -
99A ALA 3.3 7.6 - - - +
100A SER* 3.7 25.6 - - - +
101A TYR* 4.1 1.7 + - - -
107A LYS* 6.1 0.4 - - + -
108A ALA* 1.3 82.2 - - - +
110A LEU* 1.3 64.6 + - - +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 5.0 3.1 - - + -
65A ASP 4.8 10.1 - - - +
86A ILE* 3.8 26.5 - - + +
87A ARG 3.1 19.5 - - - +
88A LYS* 4.0 12.6 - - + +
98A TRP* 3.1 5.8 - - - +
99A ALA 2.9 34.4 + - - +
101A TYR* 3.9 20.6 - - + +
109A GLU* 1.3 77.6 - - - +
111A GLU* 1.3 61.3 + - - +
135A THR* 3.7 37.9 - - + +
138A ALA* 4.1 9.6 - - + -
139A ALA* 4.2 5.6 - - + +
142A LEU* 3.7 9.4 - - + +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ILE* 3.6 4.2 - - - +
87A ARG 2.6 37.9 + - - +
88A LYS 4.2 0.5 - - - +
89A ARG* 3.4 16.0 + - - +
90A GLY* 2.8 30.4 + - - -
91A LYS 3.9 5.4 + - - -
92A LEU* 3.8 16.3 + - + +
96A THR* 2.6 45.0 + - + +
97A LEU 3.3 10.8 - - - +
98A TRP* 3.9 12.8 - - + -
110A LEU* 1.3 75.8 - - - +
112A ILE* 1.3 65.6 + - - +
142A LEU* 4.0 3.8 - - - -
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Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL* 5.1 4.7 - - + -
85A LEU 3.7 12.3 - - - +
86A ILE* 3.7 22.9 - - + -
92A LEU* 4.1 4.3 - - - -
96A THR* 3.2 8.6 - - - -
97A LEU* 3.0 55.2 + - + -
111A GLU* 1.3 75.8 - - - +
113A GLN* 1.3 69.3 + - - +
116A ALA* 3.6 25.6 - - + -
142A LEU* 4.1 18.6 - - + +
143A LEU* 4.0 22.4 - - + -
146A LEU* 4.1 11.9 - - + -
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Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LEU 5.1 0.4 + - - -
92A LEU* 4.0 24.8 - - + +
93A PRO* 2.8 41.9 + - - +
94A GLY* 5.0 0.6 - - - -
95A PRO 3.5 8.5 - - - +
96A THR* 4.2 1.3 - - + -
97A LEU* 4.4 0.4 - - - -
112A ILE* 1.3 81.1 - - - +
114A LYS* 1.3 64.5 + - - +
115A ASP* 3.6 15.2 - - - +
116A ALA* 2.9 25.0 + - + +
146A LEU* 3.9 4.7 - - - +
14B ARG* 2.9 32.2 + - - +
16B PHE* 4.2 4.9 - - - -
28B ASP* 3.5 11.4 + - - +
30B SER* 4.3 9.7 + - - -
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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