Contacts of the strand formed by residues 311 - 315 (chain A) in PDB entry 2YBE
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 MET 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A THR* 2.9 50.7 - - + +
255A SER* 3.7 8.1 - - - +
256A LEU 5.6 0.4 - - - +
287A THR* 3.1 5.0 - - - -
288A ALA* 2.7 54.5 + - + +
289A ASP 5.5 0.4 - - - -
290A LYS* 3.9 3.8 - - - +
291A PHE* 3.7 50.0 - - + -
306A ILE* 4.3 2.7 - - - -
310A TRP* 1.3 75.8 - - - +
312A GLY* 1.3 61.0 + - - +
313A LEU* 3.6 12.9 + - + -
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Residues in contact with GLY 312 (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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241A PHE* 3.4 36.3 - - - -
255A SER* 3.3 13.7 + - - -
285A PHE* 4.8 3.6 - - - -
286A VAL 3.6 8.7 - - - -
287A THR* 4.4 2.7 - - - -
306A ILE* 4.0 11.9 - - - +
311A MET* 1.3 70.5 - - - +
313A LEU* 1.3 69.2 + - - +
314A ASP 3.7 1.8 - - - -
1419A LA8 4.0 6.4 + - - -
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Residues in contact with LEU 313 (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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286A VAL 3.1 6.1 + - - -
288A ALA* 3.3 28.3 - - + -
290A LYS 4.2 3.6 - - - +
291A PHE* 4.1 21.8 - - + -
311A MET* 3.6 27.3 + - + -
312A GLY* 1.3 84.5 - - - +
314A ASP* 1.3 60.0 + - - +
340A GLY* 3.2 3.7 - - - -
341A VAL* 2.8 43.2 + - + +
344A TRP* 4.7 5.6 - - + -
347A PHE* 3.5 34.4 - - + +
1419A LA8 3.7 22.4 - - + +
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Residues in contact with ASP 314 (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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241A PHE* 6.2 0.7 - - - -
285A PHE* 3.3 12.7 - - - +
286A VAL* 3.0 40.2 + - + +
312A GLY 3.7 1.0 - - - -
313A LEU* 1.3 77.1 + - - +
315A CYS* 1.3 79.3 + - - +
339A VAL 3.6 11.9 - - - +
340A GLY* 3.8 8.8 - - - -
346A ALA 5.1 0.3 - - - +
347A PHE* 3.5 21.0 - - - +
349A ARG* 3.3 14.2 + - - +
350A GLY* 2.9 36.7 + - - -
351A THR 4.2 0.5 + - - -
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Residues in contact with CYS 315 (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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282A PRO* 4.5 3.8 - - + -
284A ASP 3.3 8.3 - - - +
285A PHE* 4.0 4.3 - - - -
286A VAL* 3.4 14.0 - - - +
314A ASP* 1.3 91.6 + - - +
316A GLY* 1.3 61.5 + - - +
319A SER* 3.5 17.0 - - - -
320A SER* 3.8 13.5 - - - -
323A TYR* 3.7 33.9 - - + +
339A VAL* 3.8 11.6 + - - +
349A ARG* 6.1 0.2 - - - +
350A GLY* 3.8 26.6 + - - -
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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