Contacts of the strand formed by residues 282 - 287 (chain A) in PDB entry 1YNU
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 282 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE* 3.7 23.1 - - + -
95A MET* 4.2 9.2 - - + -
116A LEU* 5.2 0.7 - - + -
117A THR 4.0 0.9 - - - -
119A GLY* 3.8 3.0 - - - +
270A SER* 3.4 5.4 + - - -
271A LEU* 3.0 53.7 + - + +
272A SER* 4.4 3.5 + - - +
277A LEU 5.0 2.8 + - - +
280A PHE* 3.7 13.9 - - + +
281A ARG* 1.3 76.1 - - - +
283A GLY* 1.3 61.8 + - - +
305A VAL* 3.9 13.9 - - + -
309A THR* 3.7 22.7 - - + -
313A LEU* 3.7 13.0 - - + -
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Residues in contact with GLY 283 (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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95A MET* 5.1 0.7 - - - -
116A LEU* 3.4 9.9 - - - +
117A THR* 2.7 39.9 + - - +
119A GLY 3.3 13.8 - - - +
120A ALA 4.1 0.2 - - - -
269A TYR 3.6 11.0 - - - -
270A SER* 4.1 0.9 - - - -
282A VAL* 1.3 77.7 - - - +
284A ALA* 1.3 66.3 + - - +
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Residues in contact with ALA 284 (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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95A MET* 4.2 12.3 - - + -
114A LEU* 3.7 22.7 - - + -
115A VAL 3.0 12.1 - - - +
116A LEU* 4.1 8.5 - - + -
117A THR* 3.5 4.5 + - - -
123A ALA* 3.8 5.0 - - - +
268A VAL* 3.5 4.0 - - - -
269A TYR* 3.0 39.7 + - + +
283A GLY* 1.3 77.9 - - - +
285A ILE* 1.3 67.9 + - - +
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Residues in contact with ILE 285 (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 HIS 3.7 0.9 - - - +
114A LEU* 3.5 5.1 - - - +
115A VAL* 2.7 41.4 + - + +
117A THR* 4.5 6.5 - - + -
123A ALA* 3.4 35.9 - - + +
126A THR* 3.9 22.4 - - + -
127A PHE* 3.2 41.3 - - + -
267A VAL 3.4 4.5 - - - +
268A VAL* 4.5 3.8 - - + -
284A ALA* 1.3 78.3 - - - +
286A TYR* 1.3 68.8 + - - +
287A SER* 4.6 4.0 - - - +
292A VAL* 5.2 0.9 - - + -
293A VAL* 6.3 1.1 - - + -
296A ALA* 4.3 16.6 - - + -
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Residues in contact with TYR 286 (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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99A MET* 4.9 2.7 - - + -
108A THR 4.4 3.4 + - - -
109A PHE* 3.5 35.0 - + + -
110A ASP* 2.8 53.5 + - - +
113A HIS* 3.5 23.3 - - + +
114A LEU* 4.0 17.3 - - + -
247A MET* 3.6 30.9 - - + +
266A HIS* 3.5 3.5 - - - +
267A VAL* 2.8 48.6 + - + +
285A ILE* 1.3 76.6 - - - +
287A SER* 1.3 65.7 + - - +
288A ASN* 3.7 14.3 + - - -
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Residues in contact with SER 287 (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 HIS* 3.1 31.9 + - - +
127A PHE* 4.6 2.5 - - - -
265A VAL 4.3 2.7 - - - -
266A HIS* 2.7 38.2 + - - -
285A ILE* 4.3 3.1 - - - +
286A TYR* 1.3 80.9 - - - +
288A ASN* 1.3 64.2 + - - +
289A ASP* 3.0 14.0 + - - +
292A VAL* 3.7 18.3 - - - +
293A VAL* 3.9 9.6 - - - +
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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