Contacts of the strand formed by residues 336 - 344 (chain A) in PDB entry 3N9V
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 TYR 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A ALA* 3.5 12.8 - - - +
294A PRO* 2.7 46.8 + - - +
295A ASP 4.4 1.6 - - - -
297A TYR* 3.5 24.2 - + - -
330A LEU* 3.7 31.9 - - + -
331A HIS* 3.4 29.9 - - - +
334A ALA* 3.5 20.2 - - + -
335A LYS* 1.3 73.6 - - - +
337A ALA* 1.3 59.8 + - - +
338A LYS 4.2 0.3 + - - -
352A TYR* 4.3 9.1 - - + -
353A VAL* 3.4 6.7 - - - +
354A LYS* 3.7 23.8 - - + -
355A GLN* 4.6 4.1 - - - +
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TYR* 1.3 72.0 - - - +
338A LYS* 1.3 68.1 + - - +
339A VAL* 3.4 2.9 + - + +
352A TYR* 3.2 4.5 - - - -
353A VAL* 2.8 37.7 + - + +
355A GLN* 3.5 34.2 - - - +
358A ALA* 4.7 9.4 - - + -
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Residues in contact with LYS 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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323A PHE* 3.7 40.9 - - + -
336A TYR 4.2 0.8 + - - -
337A ALA* 1.3 75.2 - - - +
339A VAL* 1.3 65.5 + - - +
340A LYS* 4.0 15.0 - - - +
341A LEU* 4.3 26.3 - - + +
350A LEU* 5.9 0.9 - - + -
351A LEU 3.8 8.1 - - - +
352A TYR* 3.8 13.4 - - + -
365B GLU* 5.6 1.6 - - - -
425B CYS* 3.0 40.2 - - - +
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Residues in contact with VAL 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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337A ALA* 3.9 4.3 - - + +
338A LYS* 1.3 80.5 - - - +
340A LYS* 1.3 63.6 + - - +
351A LEU* 2.7 37.4 + - + +
352A TYR 4.4 0.2 - - - -
353A VAL* 3.6 41.7 - - + +
358A ALA* 5.9 1.8 - - + -
361A ILE* 4.0 12.8 - - + -
364A VAL* 3.8 29.5 - - + +
365B GLU* 5.7 1.0 - - - +
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Residues in contact with LYS 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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338A LYS* 3.7 9.9 - - - +
339A VAL* 1.3 86.2 - - + +
341A LEU* 1.3 79.0 + - - +
342A ILE* 5.8 2.0 - - + +
350A LEU* 3.6 2.3 - - - -
351A LEU* 2.9 29.1 + - + +
364A VAL* 3.9 27.1 - - + -
365A GLU* 5.7 0.4 - - - +
366A ALA* 4.0 22.5 - - + +
385A ILE* 3.7 34.0 - - + +
340B LYS* 4.3 19.0 - - - +
365B GLU* 5.4 6.1 + - - -
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Residues in contact with LEU 341 (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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319A GLU* 3.9 42.4 - - + +
323A PHE* 4.5 16.8 - - + -
338A LYS* 4.3 19.0 - - + +
340A LYS* 1.3 90.8 + - - +
342A ILE* 1.3 79.2 + - - +
343A ARG* 4.3 1.6 - - + +
348A MET* 4.2 7.0 - - + -
349A LEU 3.6 4.0 - - - -
350A LEU* 3.5 26.7 - - + -
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Residues in contact with ILE 342 (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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340A LYS* 5.8 2.5 - - + +
341A LEU* 1.3 80.6 - - - +
343A ARG* 1.3 67.6 + - - +
347A ILE 3.8 0.9 - - - +
348A MET* 3.2 3.6 - - - +
349A LEU* 2.9 39.9 + - + +
366A ALA* 3.9 28.7 - - + +
367A GLU* 4.4 2.9 - - - +
368A THR* 3.7 28.0 - - + -
383A VAL* 4.0 20.1 - - + +
384A ALA 4.1 5.4 - - - +
385A ILE* 3.7 24.5 - - + -
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Residues in contact with ARG 343 (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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304A LEU* 4.0 24.7 - - - -
310A ALA* 5.3 1.0 + - - +
314A HIS* 2.7 80.3 + - + -
315A ASP* 4.1 3.8 + - - +
316A THR* 3.5 19.1 - - - +
319A GLU* 2.7 35.5 + - - +
341A LEU* 4.3 3.0 - - + +
342A ILE* 1.3 82.1 - - - +
344A LEU* 1.3 63.6 + - - +
345A VAL* 2.7 43.7 + - - +
347A ILE 3.1 15.0 - - - +
348A MET* 4.0 10.3 - - + -
368A THR* 4.3 7.2 - - - +
383A VAL* 4.3 2.9 - - - -
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Residues in contact with LEU 344 (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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314A HIS* 5.1 0.7 - - - -
343A ARG* 1.3 71.7 - - - +
345A VAL* 1.3 63.3 + - + +
346A GLY 2.8 17.5 + - - -
347A ILE* 3.0 25.0 + - + +
368A THR* 3.9 15.3 - - - +
369A VAL 3.5 40.4 - - - +
370A GLY* 3.7 10.3 - - - +
378A GLY* 3.9 23.5 - - - +
380A LYS 4.8 1.6 - - - +
382A GLY 4.1 7.4 - - - +
383A VAL* 3.7 15.4 - - + +
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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