Contacts of the strand formed by residues 110 - 115 (chain B) in PDB entry 2NMY
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 LEU 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B ARG* 2.9 34.7 + - + +
109B PRO* 1.3 72.2 - - - +
111B VAL* 1.3 63.8 + - - +
121B GLU* 4.3 23.8 - - + +
122B ALA* 3.4 23.8 - - - +
123B LEU* 4.1 17.5 - - + +
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Residues in contact with VAL 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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99A PHE* 5.3 0.2 - - + -
103B ILE* 4.6 11.2 - - + -
109B PRO 4.6 0.9 - - - +
110B LEU* 1.3 78.2 - - - +
112B THR* 1.3 67.7 + - - +
113B ILE* 4.5 5.6 - - + -
121B GLU* 3.5 6.6 - - - +
122B ALA* 2.9 37.5 + - + +
124B LEU* 3.8 45.5 - - + -
166B ILE* 4.3 12.8 - - + -
167B ALA* 4.1 19.1 - - + -
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Residues in contact with THR 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 VAL* 1.3 73.8 - - - +
113B ILE* 1.4 73.9 + - - +
119B LEU* 4.0 28.9 - - + -
120B LYS 3.4 9.1 + - - +
121B GLU* 4.8 5.5 + - - +
165B GLU 4.9 0.2 - - - -
167B ALA* 3.0 29.1 + - - +
168B GLY 4.8 0.5 + - - -
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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 VAL* 4.5 4.0 - - + -
112B THR* 1.4 83.5 - - - +
114B LYS* 1.4 59.9 + - - +
115B ILE* 4.4 11.4 - - + -
118B GLN 3.7 0.2 - - - +
119B LEU* 3.3 5.9 - - - -
120B LYS* 2.9 55.5 + - + +
122B ALA* 4.0 26.0 - - + -
133B ILE* 3.9 28.0 - - + -
164B ILE* 4.2 16.4 - - + -
165B GLU 3.1 13.7 - - - +
166B ILE* 4.2 14.1 - - + -
183B ASN* 5.2 0.7 - - + -
185B ILE* 4.2 14.8 - - + -
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Residues in contact with LYS 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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113B ILE* 1.4 73.3 - - - +
115B ILE* 1.3 62.3 + - - +
117B GLY* 4.2 16.8 - - - +
118B GLN 3.3 17.3 - - - +
119B LEU* 4.0 19.5 - - + -
163B ILE 4.3 0.3 - - - +
164B ILE* 3.5 7.4 - - - +
165B GLU* 2.9 64.6 + - + +
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Residues in contact with ILE 115 (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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113B ILE* 4.4 12.3 - - + -
114B LYS* 1.3 76.2 - - - +
116B GLY* 1.3 67.7 + - - +
117B GLY 3.2 1.3 - - - -
118B GLN* 3.1 21.4 + - - +
120B LYS* 4.0 20.6 - - + -
133B ILE* 5.1 5.2 - - + -
136B MET* 4.0 27.3 - - + +
138B LEU* 4.0 21.8 - - + -
162B ILE* 4.0 19.5 - - + -
163B ILE 4.1 12.8 - - - +
164B ILE* 4.4 19.3 - - + -
175B VAL* 4.3 20.0 - - + -
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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