Contacts of the strand formed by residues 118 - 123 (chain A) in PDB entry 2NNA
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 ASN 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A VAL* 1.3 79.1 - - - +
119A ILE* 1.3 63.4 + - - +
120A THR* 4.1 9.0 - - + -
164A LYS 3.4 1.6 - - - +
165A VAL* 3.3 5.7 - - - -
166A GLU* 2.9 68.8 + - + +
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Residues in contact with ILE 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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107A CYS* 4.2 3.6 - - - -
109A VAL* 3.5 29.4 - - + -
117A VAL* 4.1 14.9 + - + -
118A ASN* 1.3 77.7 - - - +
120A THR* 1.3 66.0 + - - +
121A TRP* 5.1 0.4 - - - +
132A VAL* 5.4 3.5 - - - +
134A GLU* 4.2 17.5 + - - +
147A LYS* 3.5 39.7 - - + +
149A SER* 3.5 30.3 + - - +
163A CYS* 3.7 24.7 - - - -
164A LYS 3.4 2.7 - - - +
165A VAL* 4.4 2.0 - - + -
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Residues in contact with THR 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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118A ASN* 4.9 8.1 - - + -
119A ILE* 1.3 83.5 - - - +
121A TRP* 1.3 69.7 + - - +
122A LEU* 5.1 3.1 - - - +
127A SER* 6.1 1.6 - - - -
128A VAL 5.9 0.2 - - - -
132A VAL* 5.9 1.1 - - - -
163A CYS* 3.6 5.2 - - - -
164A LYS* 2.7 56.2 + - - +
166A GLU* 6.1 0.6 - - - +
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Residues in contact with TRP 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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91A VAL* 4.3 8.3 - - + -
105A LEU* 3.7 43.5 - - + -
106A ILE 3.9 2.5 - - - -
107A CYS* 3.3 38.6 - - + -
120A THR* 1.3 82.9 - - - +
122A LEU* 1.3 70.5 + - - +
127A SER* 3.6 1.4 - - - -
128A VAL* 3.1 36.7 + - + +
132A VAL* 3.6 24.9 - - + +
149A SER* 2.8 38.6 + - - -
150A TYR 3.7 5.7 + - - -
151A LEU* 3.7 33.4 - - + -
161A TYR* 4.8 3.6 - - + -
162A ASP 3.5 17.7 - - - -
163A CYS* 4.1 13.4 - - + -
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Residues in contact with LEU 122 (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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120A THR* 5.1 6.7 - - - +
121A TRP* 1.3 86.9 - - - +
123A SER* 1.3 60.3 + - - +
124A ASN 4.1 0.2 - - - -
125A GLY* 4.1 21.3 - - - +
126A HIS 3.1 4.0 - - - +
127A SER* 3.7 28.0 - - - +
128A VAL* 4.5 1.1 - - - -
161A TYR* 3.2 11.5 - - - +
162A ASP* 2.8 49.1 + - + +
164A LYS* 4.6 16.2 - - + +
175A LEU* 3.7 31.4 - - + -
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Residues in contact with SER 123 (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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122A LEU* 1.3 72.3 - - - +
124A ASN* 1.3 70.0 + - - +
125A GLY 3.0 0.2 - - - -
126A HIS* 2.7 43.0 + - - -
128A VAL* 3.4 24.1 - - - +
159A GLU* 2.8 31.0 + - - +
160A ILE 3.5 4.5 + - - -
161A TYR* 3.7 15.1 - - - -
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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