Contacts of the strand formed by residues 132 - 137 (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 ALA 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLU* 2.6 44.2 + - + +
130B ILE* 3.5 2.4 - - - +
131B ASP* 1.3 82.5 - - + +
133B ILE* 1.3 71.1 + - - +
145B VAL* 5.5 0.4 - - + -
146B PHE 2.9 13.0 - - - +
194B MET* 5.1 0.7 - - - -
317B TYR* 5.0 0.4 - - + -
318B ILE* 3.4 27.1 - - + -
321B ASN* 3.9 14.1 - - - +
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B CYS* 4.4 2.0 - - - -
112B ASP 3.8 4.5 - - - +
113B ILE* 3.7 20.6 - - + -
130B ILE* 3.5 27.6 - - + -
132B ALA* 1.3 81.1 - - - +
134B THR* 1.3 69.2 + - - +
135B HIS* 4.7 0.4 - - + -
146B PHE* 2.7 52.7 + - + -
194B MET* 4.7 11.9 - - + -
195B LEU* 4.9 7.6 - - + -
198B TYR* 4.0 52.9 - - + +
223B ILE* 4.8 3.4 - - + -
321B ASN* 3.7 1.3 - - - -
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Residues in contact with THR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B CYS* 3.3 6.8 - - - +
112B ASP 3.3 24.5 + - - -
133B ILE* 1.3 74.9 - - - +
135B HIS* 1.3 62.8 - - - +
143B PHE* 4.1 22.4 - - + -
144B TYR 3.1 9.4 - - - +
145B VAL* 3.7 19.7 - - + +
321B ASN* 2.6 30.6 + - - +
322B ILE* 3.8 13.5 + - - +
325B VAL* 3.8 30.9 - - + +
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Residues in contact with HIS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ALA* 3.4 17.3 - - + +
110B ASN 3.5 5.8 - - - -
111B CYS* 4.1 0.9 - - + +
133B ILE* 4.7 0.7 - - + -
134B THR* 1.3 78.4 - - - +
136B TYR* 1.3 70.0 + - - +
137B ASP* 4.3 11.6 + - + +
144B TYR* 2.8 43.0 + + + +
146B PHE* 5.0 1.1 - - + -
198B TYR* 2.6 43.6 + + + +
201B LEU* 3.5 22.3 - - + +
202B TRP* 3.5 18.4 - + - -
205B LYS 5.2 2.2 + - - -
207B PRO* 5.2 3.4 - - + -
210B PHE* 3.7 19.5 - + - -
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Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL 4.4 0.9 - - - -
109B ALA* 3.2 27.0 - - - +
110B ASN* 3.0 19.5 + - - +
135B HIS* 1.3 76.1 - - - +
137B ASP* 1.3 60.8 + - - +
138B SER* 3.3 34.9 + - - -
141B ASP* 3.0 40.3 + - - -
142B ARG 3.7 5.8 - - - -
143B PHE* 3.7 40.2 - + + +
182B ARG* 4.2 3.8 + - - -
325B VAL* 3.8 17.1 - - + +
329B GLN* 3.1 43.5 + - + -
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Residues in contact with ASP 137 (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* 2.9 45.8 + - - +
108B VAL 3.9 2.5 - - - -
109B ALA* 4.3 7.8 - - - +
135B HIS* 4.4 7.4 + - + -
136B TYR* 1.3 78.1 - - - +
138B SER* 1.3 62.8 + - - +
139B ILE* 3.3 12.8 + - - +
140B ASP* 3.2 20.3 + - - +
141B ASP* 2.9 18.9 + - - -
142B ARG 3.3 6.3 + - - -
144B TYR* 3.8 13.9 - - + -
205B LYS* 3.9 14.0 - - + +
207B PRO* 5.7 0.2 - - - +
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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
------------------------------------------------------------
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