Contacts of the strand formed by residues 115 - 121 (chain A) in PDB entry 1ZXN
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 LEU 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A THR* 3.7 4.5 - - + +
110A ASP* 2.8 41.7 + - + +
113A ASN* 3.9 26.7 - - + +
114A ASN* 1.3 74.1 - - - +
116A ILE* 1.3 67.3 + - - +
117A SER* 6.3 0.2 - - - -
218A THR* 3.6 32.3 - - + -
219A PHE* 3.7 8.1 - - - +
220A GLN* 3.5 28.3 - - + +
231A LEU* 4.8 0.7 - - - +
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Residues in contact with ILE 116 (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 PHE* 3.9 11.4 - - + -
107A VAL* 5.4 0.4 - - + -
108A THR 3.2 8.3 - - - +
109A ILE* 3.8 32.1 - - + -
115A LEU* 1.3 78.1 - - - +
117A SER* 1.3 67.9 + - - +
118A ILE* 3.5 22.7 - - + -
217A ILE 3.9 0.4 - - - +
218A THR* 3.4 2.9 - - - +
219A PHE* 3.0 64.0 + - + +
221A PRO* 4.4 10.8 - - + -
231A LEU* 3.9 12.8 - - + -
239A MET* 3.9 20.0 - - + -
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Residues in contact with SER 117 (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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106A ARG 3.7 2.6 + - - +
107A VAL* 3.5 2.3 - - - -
108A THR* 2.8 54.4 + - - +
115A LEU* 6.4 0.4 - - - -
116A ILE* 1.3 79.1 - - - +
118A ILE* 1.3 64.8 + - - +
119A TRP* 5.8 0.7 - - - +
216A CYS* 4.5 9.2 - - - -
217A ILE 3.1 7.0 - - - -
218A THR* 3.8 21.1 - - - -
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Residues in contact with ILE 118 (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 PHE* 4.2 10.8 - - + -
88A ILE* 3.9 30.7 - - + +
89A LEU* 4.6 9.2 - - + -
92A ALA* 3.7 30.1 - - + -
105A ILE* 4.2 11.9 - - + -
106A ARG 3.7 2.7 - - - -
107A VAL* 4.6 15.0 - - + +
116A ILE* 3.5 25.8 - - + -
117A SER* 1.3 82.8 - - - +
119A TRP* 1.3 63.0 + - - +
120A ASN* 5.2 1.7 - - - +
215A THR 3.9 0.7 - - - +
216A CYS* 3.3 4.7 - - - -
217A ILE* 2.9 29.5 + - - +
219A PHE* 4.1 12.8 - - + -
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Residues in contact with TRP 119 (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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104A CYS* 3.6 26.9 - - - -
105A ILE* 3.4 9.4 - - - +
106A ARG* 2.9 54.5 + - + +
117A SER* 5.8 1.1 - - - +
118A ILE* 1.3 75.6 - - - +
120A ASN* 1.3 65.8 + - - +
121A ASN* 3.7 29.6 - - + -
214A TYR* 3.4 39.9 - + + -
215A THR 3.3 7.0 - - - -
216A CYS* 3.8 27.1 - - + -
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Residues in contact with ASN 120 (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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92A ALA* 4.3 12.5 - - + +
95A ASN* 3.5 20.4 - - - +
102A MET* 4.4 5.6 - - - -
104A CYS 3.8 7.9 - - - +
105A ILE* 4.3 11.7 - - + -
118A ILE* 5.2 1.7 - - - +
119A TRP* 1.3 87.3 - - - +
121A ASN* 1.3 71.1 + - - +
122A GLY 5.4 0.4 + - - -
123A LYS 5.2 1.0 + - - -
214A TYR* 3.2 8.2 - - - +
215A THR* 3.0 47.2 + - - +
901A ADP 3.0 31.4 + - - -
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Residues in contact with ASN 121 (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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95A ASN* 3.6 1.4 + - - -
101A LYS 4.2 0.7 - - - +
102A MET* 3.0 22.2 - - - +
103A SER* 2.5 46.8 + - - -
104A CYS* 2.8 36.4 + - - +
119A TRP* 3.7 17.0 - - + -
120A ASN* 1.3 86.7 + - - +
122A GLY* 1.3 62.1 + - - +
212A GLU* 6.3 1.6 - - + -
213A ASP 3.5 10.5 - - - +
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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