Contacts of the strand formed by residues 96 - 103 (chain B) 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 THR 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B LEU* 4.1 22.0 - - + +
93B PRO 4.3 3.1 - - - +
94B GLY 3.4 12.7 + - - +
95B PRO* 1.3 79.5 - - - +
97B LEU* 1.3 67.1 + - - +
98B TRP* 3.4 30.2 - - - -
111B GLU* 4.0 17.1 + - - +
112B ILE 3.2 17.0 - - - +
113B GLN* 4.1 6.5 - - - -
114B LYS* 3.4 19.0 - - - +
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Residues in contact with LEU 97 (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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96B THR* 1.3 79.7 - - - +
98B TRP* 1.3 62.9 + - - +
111B GLU* 3.1 4.7 - - - +
112B ILE* 2.9 34.4 + - + -
114B LYS* 3.9 24.5 - - + +
142B LEU* 3.5 17.4 - - + +
145B ARG* 3.5 53.2 - - + +
146B LEU* 3.6 26.9 - - + -
1030B CL 4.0 5.4 - - + -
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Residues in contact with TRP 98 (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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89B ARG* 3.4 43.1 - - - +
96B THR* 3.4 37.2 - - - -
97B LEU* 1.3 74.6 - - - +
99B ALA* 1.3 62.6 + - - +
100B SER 5.6 0.4 - - - -
109B GLU* 3.2 23.1 + - - +
110B LEU 3.1 14.6 - - - +
111B GLU* 4.0 8.3 - - + -
142B LEU* 3.6 2.9 - - - -
145B ARG* 3.0 18.7 + - - -
1030B CL 3.7 22.4 - - + +
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Residues in contact with ALA 99 (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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98B TRP* 1.3 74.6 - - - +
100B SER* 1.3 63.5 + - - +
101B TYR* 4.1 3.8 - - - -
109B GLU* 3.4 4.2 - - - -
110B LEU* 3.0 29.8 + - - +
138B ALA* 4.2 11.7 - - + +
141B GLU* 3.4 36.1 - - - +
142B LEU* 3.9 20.0 - - + -
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Residues in contact with SER 100 (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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98B TRP* 5.6 0.8 - - - -
99B ALA* 1.3 76.7 - - - +
101B TYR* 1.3 65.4 + - - +
107B LYS* 4.0 21.8 - - - +
108B ALA 3.2 11.4 + - - -
109B GLU* 4.2 15.4 + - - +
138B ALA* 5.1 0.5 - - - +
141B GLU* 4.8 5.4 - - - +
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Residues in contact with TYR 101 (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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88B LYS* 5.3 5.0 + - - -
99B ALA 4.1 3.6 - - - -
100B SER* 1.3 77.1 + - - +
102B SER* 1.3 70.4 + - - +
103B LEU* 3.9 22.6 - - + +
107B LYS* 3.3 16.1 - - - +
108B ALA* 2.8 62.5 + - + +
109B GLU 4.1 0.9 - - - -
110B LEU* 3.7 33.1 - - + +
134B GLY* 3.7 21.3 - - - +
135B THR* 3.6 31.7 + - - +
138B ALA* 3.7 20.0 - - + -
1032B AMP 4.7 0.4 - - - -
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Residues in contact with SER 102 (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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101B TYR* 1.3 81.7 - - - +
103B LEU* 1.3 62.5 + - - +
104B GLU 4.2 9.6 + - - -
105B TYR 5.6 0.3 - - - -
106B GLY 3.5 11.5 + - - -
107B LYS* 4.0 19.3 - - - +
132B THR* 5.1 4.5 + - - -
134B GLY* 4.8 8.2 - - - -
1032B AMP 5.2 0.7 + - - -
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Residues in contact with LEU 103 (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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101B TYR* 3.9 28.7 + - + +
102B SER* 1.3 74.7 + - - +
104B GLU* 1.3 96.2 + - + +
105B TYR 3.0 4.0 + - - -
106B GLY* 3.0 20.2 + - - +
107B LYS 5.1 0.9 - - - -
108B ALA* 4.2 18.6 - - + +
135B THR* 4.6 3.8 - - - +
1032B AMP 4.5 28.7 - - + +
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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