Contacts of the strand formed by residues 334 - 340 (chain A) in PDB entry 6WLY
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 ILE 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A LYS* 3.8 37.2 - - + +
328A GLY 3.4 9.6 - - - +
329A GLU* 4.0 13.7 - - + +
333A GLY* 1.3 79.2 - - - +
335A VAL* 1.3 65.3 + - - +
336A CYS* 3.9 23.3 - - - -
349A VAL 3.9 0.2 - - - +
350A LYS* 3.4 5.2 - - - +
351A LYS* 2.9 54.1 + - + +
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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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326A LYS* 3.7 2.8 - - - +
327A ILE* 2.8 52.2 + - + +
328A GLY* 2.9 20.8 + - - +
329A GLU 6.0 0.4 - - - -
330A GLY* 5.8 3.1 - - - +
333A GLY 5.8 0.2 - - - -
334A ILE* 1.3 80.9 - - - +
336A CYS* 1.3 63.1 + - - +
348A ALA* 4.4 13.9 - - + -
349A VAL 3.5 7.2 - - - +
350A LYS* 4.2 21.8 - - + -
395A MET* 6.0 3.4 - - - -
458A ASP* 5.6 3.1 - - - +
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Residues in contact with CYS 336 (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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324A PHE* 4.3 15.9 - - + -
325A ILE 3.2 12.1 - - - +
326A LYS* 3.9 17.7 - - - -
327A ILE* 4.2 3.1 - - - +
334A ILE* 3.9 22.7 - - - -
335A VAL* 1.3 76.8 - - - +
337A ILE* 1.3 68.1 + - - +
348A ALA* 3.2 6.6 - - - +
349A VAL* 2.8 40.5 + - + +
351A LYS* 4.0 22.2 - - - -
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Residues in contact with ILE 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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323A ASN 3.5 2.4 - - - +
324A PHE* 3.3 5.4 - - - -
325A ILE* 2.9 45.1 + - + +
327A ILE* 3.5 30.0 - - + +
336A CYS* 1.3 74.1 - - - +
338A ALA* 1.3 71.6 + - - +
339A THR* 5.6 0.2 - - - +
346A LEU* 4.3 25.1 - - + -
347A VAL 3.5 9.2 - - - +
348A ALA* 4.7 0.2 - - - +
397A PHE* 3.3 40.2 - - + -
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Residues in contact with ALA 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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321A LEU* 4.0 32.1 - - + -
322A ASP 3.6 11.7 - - - +
323A ASN 4.1 2.5 - - - -
324A PHE* 4.3 11.4 - - + -
337A ILE* 1.3 79.2 - - - +
339A THR* 1.3 62.9 + - - +
346A LEU* 3.3 5.7 - - - +
347A VAL* 2.9 34.6 + - + +
349A VAL* 4.1 11.7 - - + -
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Residues in contact with THR 339 (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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321A LEU* 3.4 4.3 - - - -
322A ASP* 2.8 52.4 + - + +
323A ASN* 4.3 12.3 + - - +
337A ILE* 5.6 0.3 - - - +
338A ALA* 1.3 72.2 - - - +
340A VAL* 1.3 75.4 + - - +
341A ARG* 3.3 3.2 + - - +
344A GLY* 3.8 23.1 - - - +
345A LYS 3.4 2.9 - - - -
346A LEU* 3.4 16.2 - - + +
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Residues in contact with VAL 340 (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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320A TYR* 3.8 18.6 - - + +
321A LEU* 3.9 16.2 - - + -
338A ALA 4.0 0.2 + - - -
339A THR* 1.3 70.2 - - - +
341A ARG* 1.3 58.5 + - - +
342A SER* 3.5 19.7 - - - +
343A SER* 3.2 22.4 - - - +
344A GLY* 2.7 33.4 + - - -
345A LYS* 2.6 22.9 + - + +
347A VAL* 4.0 22.7 - - + -
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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