Contacts of the strand formed by residues 108 - 115 (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 VAL 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ARG* 3.4 29.4 - - - +
106A VAL* 3.8 15.3 - - + +
107A ARG* 1.3 74.2 - - - +
109A ALA* 1.3 63.3 + - - +
136A TYR* 4.2 2.3 - - - +
137A ASP* 4.0 0.2 - - - -
138A SER* 2.9 38.5 + - - +
209A ILE* 3.2 23.1 - - + +
211A THR* 3.7 23.8 - - + -
329A GLN* 4.5 11.2 + - - +
338A ILE* 4.1 21.1 - - + -
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Residues in contact with ALA 109 (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* 4.1 0.9 - - + -
108A VAL* 1.3 74.4 - - - +
110A ASN* 1.3 56.9 + - - +
135A HIS* 3.6 25.6 - - + +
136A TYR 3.2 15.3 - - - +
137A ASP* 4.5 6.5 - - - +
207A PRO* 4.0 15.0 - - + -
209A ILE 3.0 5.7 + - - -
210A PHE* 3.3 14.8 - - + -
211A THR* 2.8 34.7 + - - +
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Residues in contact with ASN 110 (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* 1.3 75.2 - - - +
111A CYS* 1.3 63.4 + - - +
135A HIS* 3.5 0.7 - - - -
136A TYR* 2.9 39.5 + - - -
210A PHE* 4.1 3.4 - - - -
211A THR* 3.1 31.2 - - + +
212A GLY* 4.0 3.1 - - - +
325A VAL* 3.0 41.1 + - - +
328A VAL* 3.7 18.2 - - + +
329A GLN* 2.7 27.4 + - - +
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Residues in contact with CYS 111 (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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110A ASN* 1.3 78.0 + - - +
112A ASP* 1.3 68.3 + - - +
113A ILE* 4.3 7.6 - - - -
133A ILE* 4.3 3.8 - - + -
134A THR 3.1 15.3 - - - +
135A HIS* 3.9 5.8 - - + +
198A TYR* 3.6 24.9 - - - +
210A PHE* 3.8 17.7 - - + -
211A THR 3.6 4.6 + - - -
212A GLY* 4.2 6.1 - - - -
213A TRP 5.1 0.3 + - - -
215A ILE* 3.9 17.6 - - - +
219A ASP* 4.0 7.3 - - - +
223A ILE* 4.0 21.5 - - - -
325A VAL* 4.2 4.2 - - - -
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Residues in contact with ASP 112 (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* 1.3 78.9 - - - +
113A ILE* 1.3 73.3 + - - +
114A GLU* 4.0 8.0 - - - +
133A ILE* 3.7 0.3 - - - -
134A THR 3.2 21.1 + - - -
213A TRP* 5.3 8.9 + - - +
219A ASP* 3.3 10.5 - - - +
287A LEU* 4.4 8.8 - - - +
321A ASN* 3.2 17.8 - - - +
324A ASP* 3.7 26.5 - - - +
325A VAL* 3.5 20.4 - - + +
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Residues in contact with ILE 113 (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 1.8 - - - -
112A ASP* 1.3 86.0 - - - +
114A GLU* 1.3 69.0 + - - +
115A VAL* 3.7 23.6 - - + -
130A ILE* 3.9 8.5 - - + -
132A ALA 3.2 9.9 - - - +
133A ILE* 3.9 19.7 - - + -
218A PHE* 3.9 23.0 - - + -
219A ASP* 3.0 16.4 + - - +
222A TYR* 4.0 27.8 - - + -
223A ILE* 3.4 37.7 - - + -
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Residues in contact with GLU 114 (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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112A ASP* 4.0 7.1 - - - +
113A ILE* 1.3 79.6 - - - +
115A VAL* 1.3 61.6 + - - +
130A ILE* 3.3 8.5 - - - +
131A ASP* 2.9 25.0 + - - +
132A ALA* 2.9 19.9 + - + -
218A PHE* 6.1 0.2 - - - -
317A TYR* 3.1 38.6 + - + +
320A TYR* 6.0 0.7 - - - +
321A ASN* 3.2 42.9 + - + +
324A ASP* 4.4 7.4 - - - +
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Residues in contact with VAL 115 (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* 3.7 26.5 - - + -
114A GLU* 1.3 80.8 + - - +
116A THR* 1.3 62.6 + - - +
117A GLY 3.6 2.1 + - - -
121A PRO* 3.7 27.4 - - + +
128A TYR* 3.4 19.7 - - + +
129A GLU 3.7 11.2 - - - +
130A ILE* 3.8 11.4 - - + -
218A PHE* 4.6 5.7 - - + -
222A TYR* 3.3 37.5 - - + +
317A TYR* 3.9 2.2 + - - -
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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