Contacts of the strand formed by residues 130 - 137 (chain A) in PDB entry 1NOY
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 ILE 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE* 3.9 18.2 - - + -
114A GLU 3.3 16.2 - - - +
115A VAL* 3.8 13.5 - - + -
128A TYR 3.5 1.2 + - - -
129A GLU* 1.3 70.9 - - - +
131A ASP* 1.3 58.5 + - - +
132A ALA 3.6 9.0 - - - +
133A ILE* 3.1 40.6 - - + -
148A LEU* 3.8 6.5 - - - +
191A GLU* 3.2 15.1 + - - +
194A MET* 3.0 33.8 - - + +
195A LEU* 4.1 16.2 - - + -
222A TYR* 4.6 6.1 - - + -
223A ILE* 6.0 4.7 - - + -
226A ARG* 4.3 12.8 - - + -
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Residues in contact with ASP 131 (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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114A GLU 2.9 6.9 + - - +
116A THR* 2.9 35.9 + - - +
129A GLU 3.3 5.0 + - - +
130A ILE* 1.3 72.3 - - - +
132A ALA* 1.3 62.8 + - - +
147A ASP* 3.8 5.7 - - - +
148A LEU* 3.2 32.2 + - + +
151A SER* 4.2 12.2 + - - +
153A TYR* 5.7 0.7 - - - +
194A MET* 4.6 0.7 - - - -
310A ARG* 3.8 27.6 + - - +
317A TYR* 2.4 37.9 + - - -
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Residues in contact with ALA 132 (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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113A ILE* 3.2 2.8 - - - +
114A GLU* 2.9 47.3 + - + -
130A ILE* 3.5 5.2 + - - +
131A ASP* 1.3 80.3 - - - +
133A ILE* 1.3 70.5 + - - +
145A VAL* 6.2 0.7 - - + -
146A PHE 3.3 11.2 - - - +
147A ASP* 5.2 0.4 - - - +
194A MET* 4.5 0.2 - - - +
317A TYR* 4.3 9.0 - - + -
318A ILE* 4.3 13.5 - - + -
321A ASN* 4.1 10.8 - - - +
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Residues in contact with ILE 133 (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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111A CYS* 4.3 4.7 - - - -
112A ASP 3.7 5.4 - - - +
113A ILE* 3.9 18.4 - - + -
130A ILE* 3.1 33.4 - - + -
132A ALA* 1.3 73.0 - - - +
134A THR* 1.3 71.4 + - - +
144A TYR 3.2 2.9 - - - +
145A VAL* 3.5 1.2 - - - +
146A PHE* 2.8 48.4 + - + -
194A MET* 4.6 5.4 - - + -
195A LEU* 4.4 12.3 - - + -
198A TYR* 3.8 53.6 - - + -
223A ILE* 5.3 3.1 - - + -
321A ASN* 3.9 0.4 - - - +
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Residues in contact with THR 134 (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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111A CYS* 3.1 25.0 - - - +
112A ASP 3.2 10.2 + - - -
133A ILE* 1.3 74.4 + - - +
135A HIS* 1.3 61.9 + - - +
136A TYR 4.1 0.4 - - - -
143A PHE* 4.2 12.8 - - + -
144A TYR 3.1 7.9 - - - +
145A VAL* 4.1 13.3 - - + +
321A ASN* 2.4 29.2 + - - +
322A ILE* 3.9 27.8 - - + +
325A VAL* 3.5 33.2 - - + +
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Residues in contact with HIS 135 (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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109A ALA* 3.6 26.7 - - + +
110A ASN 3.5 4.5 - - - -
111A CYS* 3.9 2.6 - - + +
133A ILE* 4.7 0.2 - - + -
134A THR* 1.3 76.4 - - - +
136A TYR* 1.3 67.0 + - - +
137A ASP* 4.4 12.1 + - + +
143A PHE* 4.5 0.7 - - - -
144A TYR* 2.8 41.9 + + - +
146A PHE* 4.6 1.1 - - + -
198A TYR* 2.9 38.7 + + + -
201A LEU* 3.9 25.9 - - + +
202A TRP* 3.8 20.9 - + - -
205A LYS* 5.1 4.1 + - - +
207A PRO* 4.6 5.2 - - + +
210A PHE* 3.8 12.0 - + - -
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Residues in contact with TYR 136 (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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108A VAL 4.6 1.1 - - - -
109A ALA* 3.2 26.5 - - - +
110A ASN* 2.9 32.7 + - - +
135A HIS* 1.3 75.6 - - - +
137A ASP* 1.3 61.5 + - - +
138A SER* 3.6 31.0 + - - -
141A ASP* 2.9 44.9 + - - -
142A ARG 3.5 10.8 - - - -
143A PHE* 3.7 32.1 - + + +
182A ARG* 4.3 4.0 + - - -
325A VAL* 3.7 18.3 - - + +
329A GLN* 3.5 32.2 + - + -
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Residues in contact with ASP 137 (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 ARG* 2.9 37.4 + - - +
108A VAL 4.0 2.7 - - - -
109A ALA* 4.5 3.0 - - - +
135A HIS* 4.5 10.9 + - + -
136A TYR* 1.3 78.4 - - - +
138A SER* 1.3 52.9 + - - +
139A ILE* 2.7 34.1 + - - +
140A ASP* 3.0 15.4 + - + -
141A ASP* 2.7 35.7 + - - -
142A ARG 3.2 5.9 + - - -
144A TYR* 4.2 19.7 - - + -
201A LEU* 5.9 0.6 - - + +
205A LYS* 3.7 11.1 - - - +
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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