Contacts of the strand formed by residues 333 - 338 (chain A) in PDB entry 3MYV
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 LYS 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A GLN* 4.9 3.0 + - - -
329A LYS* 3.3 11.5 - - - +
330A TYR 2.9 33.5 + - - +
331A ALA* 4.0 9.0 - - + +
332A GLY* 1.3 83.3 - - - +
334A THR* 1.3 67.5 + - - +
335A VAL* 3.5 3.5 + - + -
439A GLY 2.8 30.7 + - - -
440A TYR* 4.0 19.2 - - + +
258B GLU* 3.7 23.8 - - - +
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Residues in contact with THR 334 (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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327A GLU* 3.4 38.3 + - + +
328A ASN 3.4 5.8 - - - +
329A LYS* 2.7 28.8 + - - +
333A LYS* 1.3 75.1 - - - +
335A VAL* 1.3 69.4 + - - +
336A TRP* 3.8 27.2 - - + -
440A TYR* 3.6 14.6 - - - -
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Residues in contact with VAL 335 (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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297A TRP* 3.9 20.0 - - + -
304A PHE* 4.3 16.4 - - + -
327A GLU* 3.5 4.5 - - - +
328A ASN 2.9 36.8 + - - +
330A TYR* 3.8 37.2 - - + +
333A LYS* 3.5 4.2 + - + +
334A THR* 1.3 81.1 - - - +
336A TRP* 1.3 69.5 + - - +
440A TYR* 3.7 40.4 - - + -
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Residues in contact with TRP 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 3.2 9.6 - - - +
305A VAL* 3.0 40.2 + - + +
307A GLN* 4.6 11.2 - - + -
310A ALA* 3.4 23.3 - - + -
311A GLU* 5.7 5.2 - - + -
314A LEU* 3.4 32.9 - - + +
325A LEU* 4.4 16.8 - - + -
326A GLU 3.3 6.5 - - - +
327A GLU* 3.8 36.5 + - + +
334A THR* 3.8 36.3 - - + -
335A VAL* 1.3 80.5 - - - +
337A TRP* 1.3 60.2 + - - +
440A TYR* 3.1 20.6 + + - -
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Residues in contact with TRP 337 (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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295A LEU 3.6 13.0 - - - +
296A ASN* 3.6 27.4 - - - -
297A TRP* 3.3 39.5 - + + +
298A TYR* 3.8 24.5 + + - -
303A GLY 4.3 5.8 - - - +
304A PHE* 4.2 21.5 - - + +
305A VAL* 4.7 3.1 - - - -
325A LEU* 3.5 5.5 - - - +
326A GLU* 2.9 73.4 + - + +
327A GLU 4.9 0.6 + - - -
328A ASN* 4.6 10.3 - - + +
335A VAL* 6.1 0.2 - - + -
336A TRP* 1.3 76.2 - - - +
338A LEU* 1.3 81.8 + - - +
339A TYR* 3.5 41.2 + + + -
346A LEU* 4.3 7.0 - - + -
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Residues in contact with LEU 338 (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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74A MSE 3.8 27.4 - - + +
295A LEU* 4.2 24.8 + - + +
303A GLY 5.3 0.6 + - - -
304A PHE* 5.1 0.4 - - - +
305A VAL* 3.8 8.7 - - + +
309A TYR* 5.3 0.2 - - + -
321A ARG 5.8 0.4 - - - +
324A LEU* 3.9 13.5 - - + +
325A LEU* 3.9 18.8 - - + -
337A TRP* 1.3 85.0 - - - +
339A TYR* 1.3 61.4 + - - +
340A LYS* 3.4 24.9 + - + -
341A LEU* 5.0 1.6 + - + +
418A VAL* 3.8 27.6 - - + +
419A GLY* 3.6 31.9 - - - +
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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