Contacts of the strand formed by residues 351 - 356 (chain D) in PDB entry 6WNX
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 351 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D HIS* 3.9 11.2 - - - +
330D GLU* 4.0 16.6 + - - +
346D GLY* 3.6 1.6 - - - -
347D ALA* 3.1 25.5 + - - +
349D ASP* 3.2 35.3 + - - +
350D GLY* 1.3 78.7 - - - +
352D ILE* 1.3 61.3 + - - +
353D LYS* 5.4 5.7 - - + +
374D THR* 4.1 27.4 - - + +
375D LEU 3.7 4.5 - - - -
376D VAL* 4.0 30.1 - - + +
382D VAL* 4.1 0.2 - - - +
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Residues in contact with ILE 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D VAL* 3.7 24.2 - - + -
345D SER 3.2 14.4 - - - +
346D GLY* 4.2 9.0 - - - -
350D GLY 5.1 0.9 - - - +
351D LYS* 1.3 77.9 - - - +
353D LYS* 1.3 66.3 + - - +
373D ARG 4.0 0.3 - - - +
374D THR* 3.5 2.9 - - - +
375D LEU* 2.7 61.4 + - + +
378D HIS* 4.4 7.2 - - + -
382D VAL* 4.4 8.7 - - + -
385D LEU* 4.5 6.1 - - + -
392D ILE* 4.6 4.5 - - + -
394D SER* 3.6 33.0 - - - +
404D TRP* 4.0 21.8 - - + +
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Residues in contact with LYS 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D GLY* 3.6 29.9 + - - -
329D HIS* 3.5 22.8 - - + +
330D GLU* 6.1 0.7 - - - -
344D VAL* 3.3 7.1 - - - +
345D SER* 2.9 36.3 + - - +
351D LYS* 5.4 6.4 - - - +
352D ILE* 1.3 77.1 - - - +
354D VAL* 1.3 62.3 + - - +
355D TRP* 3.5 40.0 - - + +
371D CYS* 3.8 15.7 - - - +
373D ARG 3.4 3.8 - - - +
374D THR* 3.2 35.9 + - + +
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Residues in contact with VAL 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D TRP* 4.0 22.2 - - + +
342D ARG* 3.6 32.1 - - + -
343D ILE 3.4 6.3 - - - +
344D VAL* 4.4 12.1 - - + -
353D LYS* 1.3 78.2 - - - +
355D TRP* 1.3 57.7 + - - +
371D CYS* 3.6 3.8 - - - -
372D LEU* 2.8 43.2 + - + +
373D ARG* 3.0 22.2 + - + +
375D LEU* 4.0 26.0 - - + -
392D ILE* 4.5 0.2 - - + -
406D PHE* 5.7 0.7 - - + -
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Residues in contact with TRP 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D ILE* 3.7 18.8 - - + +
326D LEU* 3.9 39.5 - - + -
327D GLU 3.4 33.0 - - - -
328D GLY* 4.4 1.6 - - - -
329D HIS* 4.2 5.8 - + - -
342D ARG* 3.0 24.6 - - - +
343D ILE* 2.8 47.8 + - + +
345D SER* 2.8 24.5 + - - -
353D LYS* 3.5 37.4 - - + +
354D VAL* 1.3 75.6 - - - +
356D ASP* 1.3 62.7 + - - +
357D LEU* 3.1 4.6 + - - -
360D ALA* 5.9 0.7 - - + -
367D ALA 5.9 0.4 - - - -
370D LEU* 3.2 10.3 - - + +
371D CYS* 3.8 32.5 - - + -
372D LEU* 4.2 3.1 - - - -
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Residues in contact with ASP 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D LYS 3.8 8.6 - - - +
355D TRP* 1.3 66.9 - - - +
357D LEU* 1.3 66.8 + - - +
358D GLN* 3.2 16.6 + - - +
359D ALA* 3.3 28.1 + - + +
360D ALA* 3.0 21.0 + - - +
369D THR 5.2 1.3 - - - +
370D LEU* 2.9 16.8 + - - +
372D LEU* 3.8 30.3 - - + +
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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