Contacts of the strand formed by residues 282 - 286 (chain A) in PDB entry 4Y6O
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 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A VAL* 5.8 1.3 - - - -
256A LEU* 5.0 0.7 - - - -
257A LEU* 3.4 37.0 - - + +
259A VAL* 5.3 2.0 - - + -
273A ILE* 3.0 37.9 + - - +
274A SER* 4.1 4.4 - - - +
280A THR 3.5 8.5 - - - +
281A PRO* 1.3 80.0 - - - +
283A LEU* 1.3 60.5 + - - +
305A GLY 4.6 1.2 + - - -
306A GLY 3.1 22.4 + - - -
307A MET* 3.6 26.7 - - + +
316A ARG* 3.0 38.5 + - - +
317A ASP* 2.8 41.5 + - - +
318A VAL* 2.9 26.7 + - - +
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Residues in contact with LEU 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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64A LEU* 3.8 33.9 - - + -
67A VAL* 4.0 23.1 - - + -
256A LEU* 4.6 2.1 - - + +
257A LEU 2.9 7.7 + - - +
258A LEU* 3.6 29.8 - - + +
259A VAL* 2.8 32.6 + - - +
281A PRO 4.3 0.2 - - - -
282A ARG* 1.3 73.2 - - - +
284A LEU* 1.3 63.5 + - - +
285A ILE* 4.0 14.7 + - + +
307A MET* 4.5 2.9 - - - -
318A VAL* 3.4 31.4 - - + +
320A TRP* 4.4 5.6 - - + +
331A LEU* 3.8 14.8 - - + -
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Residues in contact with LEU 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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259A VAL* 3.3 36.3 - - + +
260A MET* 5.4 0.2 - - - -
262A THR 3.8 17.5 - - - +
264A LEU* 5.8 2.0 - - + -
282A ARG 4.1 0.6 + - - -
283A LEU* 1.3 73.4 - - - +
285A ILE* 1.3 59.4 + - - +
286A ASN* 3.8 14.1 - - + +
288A GLU 3.8 20.2 - - - +
289A LYS* 4.0 16.4 - - - +
307A MET* 3.8 18.6 - - + +
309A PHE* 3.7 20.9 - - + -
318A VAL 2.8 13.1 + - - +
319A ALA* 3.6 6.5 - - + -
320A TRP* 2.8 32.3 + - - +
321A LEU* 5.0 2.5 - - + -
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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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64A LEU* 5.3 1.3 - - + -
258A LEU* 5.0 1.8 - - + -
259A VAL 2.8 8.7 + - - -
260A MET* 3.2 31.0 - - + -
261A GLY 2.9 24.9 + - - -
283A LEU* 4.0 26.7 - - + +
284A LEU* 1.3 74.8 - - - +
286A ASN* 1.3 60.4 + - - +
320A TRP* 3.5 20.9 - - + -
323A GLU 4.4 1.1 - - - +
324A CYS* 3.6 25.4 - - + +
327A GLY* 3.8 39.7 - - - +
328A CYS* 4.4 3.8 - - - +
331A LEU* 4.6 9.0 - - + -
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Residues in contact with ASN 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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86A GLY* 5.2 1.2 - - - -
261A GLY* 3.2 23.4 - - - -
262A THR 3.3 26.5 + - - -
263A SER* 4.0 8.5 - - - +
284A LEU* 3.8 18.4 - - + +
285A ILE* 1.3 75.7 - - - +
287A LYS* 1.3 78.6 + - - +
288A GLU* 3.0 35.5 + - - +
320A TRP 3.2 5.5 + - - +
321A LEU* 3.2 10.9 - - - +
322A GLY 3.0 23.6 + - - -
324A CYS* 4.9 2.2 - - - -
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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
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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