Contacts of the strand formed by residues 382 - 388 (chain A) 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 VAL 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A ARG* 3.1 26.5 - - - +
335A CYS* 3.6 21.4 - - - -
346A GLY* 4.0 10.3 - - - -
347A ALA 3.4 19.1 + - - +
350A GLY* 3.7 25.6 - - - +
351A LYS 4.1 7.9 - - - +
352A ILE* 4.3 12.1 - - + -
378A HIS* 4.0 18.8 - - + -
380A GLY 4.1 0.2 - - - +
381A ARG* 1.3 71.9 - - - +
383A PHE* 1.3 60.3 + - - +
384A ARG 4.1 6.1 - - - +
385A LEU* 4.8 0.2 - - + -
394A SER* 4.5 4.5 - - - -
395A SER 3.5 16.2 - - - +
396A SER* 4.4 0.2 - - - +
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Residues in contact with PHE 383 (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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128A LYS 5.7 0.2 - - - -
129A GLY* 4.7 2.2 - - - -
130A VAL 3.3 32.3 - - - +
131A TYR* 3.4 39.7 - + - +
145A ARG* 6.3 0.2 - - - -
334A ARG* 3.1 43.8 + - + +
335A CYS* 3.7 8.9 - - - +
381A ARG* 3.9 18.8 - - + -
382A VAL* 1.3 75.5 - - - +
384A ARG* 1.3 66.7 + - - +
395A SER 3.0 5.9 + - - -
396A SER 3.8 0.4 - - - -
397A HIS* 3.4 51.6 - + + -
32C ASP* 3.5 32.1 - - - -
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Residues in contact with ARG 384 (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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131A TYR 3.7 8.3 - - - +
132A CYS* 3.8 11.8 - - - +
133A LEU* 3.6 36.5 + - + +
173A LEU 5.7 3.1 + - - -
212A HIS* 3.4 35.2 + - - -
295A CYS* 6.3 1.2 - - - +
335A CYS* 3.7 15.0 - - - +
336A ILE 5.9 0.2 + - - -
337A ARG* 4.4 25.7 - - - +
382A VAL* 3.5 2.5 - - - +
383A PHE* 1.3 85.1 + - - +
385A LEU* 1.3 71.4 + - - +
394A SER* 3.3 2.8 - - - -
395A SER* 2.7 46.4 + - - +
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Residues in contact with LEU 385 (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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133A LEU* 4.5 1.6 - - - -
335A CYS* 3.6 27.0 - - + +
336A ILE 4.9 0.9 - - - +
337A ARG* 3.3 38.6 - - + +
344A VAL* 3.6 40.2 - - + +
345A SER 3.9 8.1 - - - +
346A GLY* 3.7 17.7 - - - +
352A ILE* 4.5 10.8 - - + -
382A VAL* 4.8 0.4 - - + -
384A ARG* 1.3 86.5 + - - +
386A GLN* 1.3 69.2 + - - +
387A PHE* 4.5 1.3 - - + -
392A ILE* 4.3 5.4 - - + -
393A ILE 3.1 13.7 - - - +
394A SER* 4.0 9.6 - - - -
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Residues in contact with GLN 386 (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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133A LEU* 4.1 9.6 - - + +
134A GLN* 3.2 17.8 - - - +
135A TYR* 3.1 73.1 + - + -
337A ARG* 4.5 9.9 - - - +
385A LEU* 1.3 77.0 - - - +
387A PHE* 1.3 68.0 + - - +
392A ILE* 3.5 1.2 - - - +
393A ILE 2.8 32.4 + - - +
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Residues in contact with PHE 387 (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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110A TRP* 3.8 8.3 - + - -
135A TYR* 3.5 6.9 + - - -
337A ARG* 3.7 15.7 - - + +
338A PHE* 3.7 24.0 - - - -
339A ASP* 3.6 43.7 - - + -
342A ARG* 3.6 22.7 - - + -
344A VAL* 3.6 31.9 - - + -
385A LEU* 4.5 1.3 - - + -
386A GLN* 1.3 83.0 + - - +
388A ASP* 1.3 73.3 + - - +
391A GLN 3.1 15.3 - - - +
392A ILE* 3.9 15.3 - - + -
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Residues in contact with ASP 388 (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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71A ARG* 4.1 2.9 + - - -
110A TRP* 3.4 17.5 - - - -
135A TYR* 2.9 23.9 + - + +
339A ASP* 4.6 7.2 - - - -
342A ARG* 5.5 0.3 + - - -
387A PHE* 1.3 83.5 - - - +
389A GLU* 1.3 66.6 - - - +
390A PHE* 3.0 26.0 + - + +
391A GLN* 2.9 33.3 + - - +
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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