Contacts of the strand formed by residues 116 - 122 (chain A) in PDB entry 1F6A
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 TYR 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ASP* 3.6 34.7 - - + +
115A VAL* 1.3 78.8 - - - +
117A LYS* 1.3 67.8 + - + +
118A VAL 3.4 0.9 - - - -
131A TYR 3.6 7.0 - - - +
132A GLU* 4.0 26.9 - - + +
153A GLY* 3.7 0.3 - - - -
154A LYS* 2.7 36.3 + - - +
156A TRP* 5.8 4.9 - + - -
371A CPS 2.9 101.9 - - + +
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Residues in contact with LYS 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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116A TYR* 1.3 73.9 - - - +
118A VAL* 1.3 63.7 + - - +
119A ILE* 3.6 7.8 + - - +
129A TYR* 3.7 28.9 - - + +
130A TRP 3.3 11.0 - - - -
131A TYR* 2.7 19.7 + - - +
132A GLU 4.2 0.2 - - - +
152A THR* 3.7 0.9 + - - +
153A GLY* 3.6 9.9 - - - -
154A LYS* 4.2 30.6 - - + +
371A CPS 3.8 28.9 + - - +
332B ASN* 5.9 0.4 - - - +
334B ARG 5.3 1.3 - - - -
335B GLY* 3.2 33.1 + - - -
337B SER* 5.3 1.2 + - - -
362B ASP* 3.4 26.7 + - - +
1G NAG 4.7 10.9 - - + +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A CYS* 3.6 32.1 - - + -
115A VAL* 3.3 28.5 - - + +
117A LYS* 1.3 71.0 - - - +
119A ILE* 1.3 65.5 + - - +
120A TYR* 4.2 7.6 - - + -
129A TYR* 3.5 0.9 - - - -
130A TRP 3.3 26.4 + - - -
132A GLU 3.7 0.2 - - - +
133A ASN* 3.2 34.8 - - - +
134A HIS* 3.3 22.6 - - + +
151A CYS* 4.6 0.2 - - + -
152A THR 3.2 10.8 - - - +
153A GLY* 4.2 0.7 - - - -
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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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117A LYS 3.6 5.1 + - - +
118A VAL* 1.3 77.4 - - - +
120A TYR* 1.3 71.6 + - - +
121A TYR* 3.6 33.3 + - + +
126A ALA* 4.6 5.6 - - + -
128A LYS 3.3 11.4 - - - +
129A TYR* 3.5 29.8 - - + -
151A CYS* 3.1 4.8 - - - +
152A THR* 2.8 45.3 + - - +
394B ASN* 3.0 33.4 - - + +
1G NAG 4.7 12.8 - - + +
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Residues in contact with TYR 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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90A LEU* 3.7 27.6 - - + -
105A LEU* 3.9 11.2 + - + -
106A ARG* 3.2 7.8 - - - -
107A CYS* 2.6 36.6 + - + +
118A VAL* 4.2 4.5 - - + -
119A ILE* 1.3 78.1 - - - +
121A TYR* 1.3 62.9 + - - +
126A ALA 3.9 0.2 - - - -
127A LEU* 2.9 34.3 + - + +
128A LYS 3.0 11.4 + - - +
134A HIS* 2.7 50.7 + + - -
136A ILE* 3.2 43.3 - - + -
149A TYR* 5.5 2.2 - + + -
150A TYR 3.6 2.2 - - - -
151A CYS* 3.8 9.4 - - + -
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Residues in contact with TYR 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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119A ILE* 3.6 29.2 - - + +
120A TYR* 1.3 75.0 - - - +
122A LYS* 1.3 60.2 - - - +
123A ASP 4.1 0.7 - - - -
124A GLY 4.3 7.6 - - - +
125A GLU 3.2 25.6 - - - +
126A ALA* 3.7 20.4 - - + -
127A LEU* 4.7 0.4 - - - -
149A TYR* 3.0 31.2 - - - +
150A TYR* 2.6 65.8 + + + +
152A THR* 3.6 27.5 + - + -
393B ARG 5.4 0.4 - - - -
394B ASN* 4.1 15.4 - - - +
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Residues in contact with LYS 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 TYR 4.3 0.2 + - - -
121A TYR* 1.3 73.6 - - - +
123A ASP* 1.3 81.4 + - - +
125A GLU* 2.9 32.7 + - + +
127A LEU* 3.7 30.4 - - + +
144A GLU* 2.8 41.1 + - - +
145A ASP* 3.1 24.4 + - - +
146A SER 3.5 11.0 - - - +
148A THR 3.6 4.0 - - - +
149A TYR* 3.5 27.7 + - + +
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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