Contacts of the strand formed by residues 108 - 114 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B ARG* 4.3 17.5 - - + +
106B VAL* 3.9 21.1 - - + +
107B ARG* 1.3 75.1 - - - +
109B ALA* 1.3 62.2 + - - +
136B TYR* 4.2 2.4 - - - +
137B ASP* 4.9 0.2 - - - -
138B SER* 2.8 46.8 + - - +
209B ILE* 3.6 12.6 - - + +
211B THR* 3.8 24.2 - - + -
329B GLN* 4.4 13.9 - - - +
338B ILE* 4.2 30.7 - - + -
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ARG 3.9 0.8 + - - +
108B VAL* 1.3 75.1 - - - +
110B ASN* 1.3 60.0 + - - +
135B HIS* 3.4 22.7 - - + +
136B TYR 3.2 18.2 - - - +
137B ASP* 4.3 8.3 - - - +
207B PRO* 3.8 21.3 - - + -
209B ILE 3.0 6.3 + - - -
210B PHE* 3.0 12.7 - - + -
211B THR* 2.8 24.9 + - - +
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Residues in contact with ASN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ALA* 1.3 73.6 - - - +
111B CYS* 1.3 62.4 + - - +
135B HIS* 3.5 2.4 - - - -
136B TYR* 3.0 39.9 + - - +
210B PHE* 3.9 2.5 - - - -
211B THR* 2.9 35.7 - - + +
212B GLY* 3.8 4.0 - - - +
325B VAL* 3.2 30.8 - - - +
328B VAL* 3.8 17.4 - - + +
329B GLN* 2.8 35.3 - - - +
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Residues in contact with CYS 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ASN* 1.3 79.8 - - - +
112B ASP* 1.3 66.0 + - - +
113B ILE* 4.0 22.4 - - - -
133B ILE* 4.4 2.7 - - + -
134B THR 3.3 14.1 - - - +
135B HIS* 4.1 3.4 - - + -
198B TYR* 3.7 16.2 - - - +
210B PHE* 3.5 28.3 - - + -
211B THR 3.4 4.9 + - - -
212B GLY* 4.3 5.7 - - - -
213B TRP 5.1 0.5 + - - -
215B ILE* 3.8 17.2 - - - +
219B ASP* 3.9 10.2 - - - +
223B ILE* 4.5 7.4 - - - -
325B VAL* 4.2 4.5 - - - -
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Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B CYS* 1.3 75.9 - - - +
113B ILE* 1.3 66.4 + - - +
134B THR 3.3 20.4 + - - -
213B TRP* 4.8 10.4 + - - +
219B ASP* 3.5 3.0 - - - +
287B LEU* 4.7 8.0 - - - +
321B ASN* 2.8 21.1 + - - +
324B ASP* 4.2 13.6 - - - +
325B VAL* 3.2 23.5 - - + +
2000B ZN 3.1 23.3 - - - -
3000B MN 2.9 30.4 + - - -
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Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B CYS* 4.0 7.0 - - - -
112B ASP* 1.3 85.4 - - - +
114B GLU* 1.3 65.4 + - - +
115B VAL* 4.0 15.4 + - + -
130B ILE* 4.1 11.2 - - + -
132B ALA 3.3 7.9 - - - +
133B ILE* 3.7 26.7 - - + -
218B PHE* 3.8 26.1 - - + -
219B ASP* 3.1 24.7 + - + +
222B TYR* 4.1 23.8 - - + -
223B ILE* 3.8 25.1 - - + -
3000B MN 4.1 6.8 + - - -
5S T 4.3 6.4 - - - +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ASP* 3.9 0.3 - - - +
113B ILE* 1.3 75.6 - - - +
115B VAL* 1.3 67.0 + - - +
130B ILE* 3.3 4.7 - - - +
131B ASP* 2.9 24.5 + - - -
132B ALA* 2.6 23.3 + - + +
317B TYR* 3.8 36.3 + - + +
320B TYR* 5.4 1.3 - - - +
321B ASN* 3.3 36.9 + - + +
2000B ZN 2.5 32.7 - - - -
5S T 3.0 26.6 - - - +
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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