Contacts of the strand formed by residues 110 - 114 (chain B) in PDB entry 3NUI
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 ARG 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 4.4 0.6 - - - +
109B GLY* 1.3 76.5 - - - +
111B VAL* 1.3 66.2 + - - +
112B PHE* 3.5 41.1 - - + -
297B VAL 3.7 0.3 - - - +
298B ILE* 3.5 2.8 - - - +
299B LEU* 2.8 34.2 + - + +
304B SER* 3.4 19.9 + - - +
307B LEU* 4.5 9.0 - - - +
308B GLU* 2.9 51.5 - - - +
311B ILE* 4.7 6.3 - - - +
317B PHE* 4.3 18.8 - - - -
323B ALA* 5.7 4.4 - - - +
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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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97B SER* 3.8 39.3 + - - +
100B LEU* 4.1 14.1 - - + -
101B VAL* 3.9 13.2 - - + -
110B ARG* 1.3 81.6 - - - +
112B PHE* 1.3 74.1 + - - +
113B TYR* 3.5 31.6 - - + +
296B ALA* 4.1 9.6 - - + -
297B VAL 3.2 9.9 - - - +
298B ILE* 4.4 7.2 - - + -
323B ALA* 3.6 23.4 - - - +
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Residues in contact with PHE 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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110B ARG* 3.5 42.6 - - + -
111B VAL* 1.3 79.5 - - - +
113B TYR* 1.3 63.7 + - - +
114B THR* 5.2 0.2 - - - -
123B THR* 5.1 8.5 - - + -
127B MET* 4.2 15.3 - - - -
296B ALA* 3.2 5.7 - - - +
297B VAL* 2.8 51.8 + - + +
299B LEU* 3.6 27.6 - - + -
307B LEU* 3.7 17.9 - - + -
317B PHE* 4.7 9.4 - + - -
321B PHE* 4.1 16.8 - + + -
322B THR 3.3 31.4 - - - +
323B ALA* 4.6 7.4 - - + -
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Residues in contact with TYR 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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93B THR* 4.3 3.4 - - + -
96B LEU* 3.5 29.2 - - + +
97B SER* 2.8 46.2 + - - -
100B LEU* 3.7 6.2 - - + +
111B VAL* 3.5 23.2 - - + +
112B PHE* 1.3 74.2 - - - +
114B THR* 1.3 72.5 - - - +
287B LEU* 5.8 0.2 - - + -
294B MET* 4.2 11.7 - - + -
295B GLY 3.5 12.6 - - - -
296B ALA* 4.2 3.4 - - + -
320B GLY 5.7 0.5 - - - +
322B THR* 2.9 28.3 + - + +
323B ALA* 3.4 18.6 - - - -
324B SER 4.5 1.1 - - - +
325B GLY* 3.3 39.3 - - - +
326B HIS 5.0 0.7 - - - +
330B CYS* 4.4 5.6 - - - -
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Residues in contact with THR 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 PHE 5.2 0.2 - - - -
113B TYR* 1.3 81.4 - - - +
115B ASN* 1.3 64.9 + - - +
116B SER 2.8 22.7 + - - -
119B GLU* 3.6 18.2 - - + +
120B ALA* 3.5 17.6 + - + +
123B THR* 3.6 29.4 - - + +
294B MET* 3.2 13.7 - - - +
295B GLY* 2.9 29.3 + - - -
297B VAL* 5.0 2.7 - - + -
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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