Contacts of the strand formed by residues 347 - 354 (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 ILE 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A PHE 3.5 5.6 - - - +
302A GLN* 4.5 2.2 - - + +
343A ARG* 3.1 3.9 - - - -
344A LEU* 3.0 42.4 + - + +
345A VAL 3.4 0.6 - - - -
346A GLY* 1.3 79.8 - - - +
348A MET* 1.3 59.0 + - - +
378A GLY 4.5 6.7 - - - +
379A ASN 5.5 1.1 - - - +
380A LYS* 4.1 6.1 - - - -
381A GLY 3.5 36.3 - - - +
382A GLY 4.3 0.9 - - - +
383A VAL* 3.7 15.2 - - + +
398A ASN* 3.6 39.7 - - - +
399A SER* 4.8 1.8 - - - -
400A HIS* 3.7 26.5 - - + +
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Residues in contact with MET 348 (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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299A VAL 3.9 0.7 - - - +
300A GLY* 3.4 0.7 - - - -
301A PHE* 2.8 67.0 + - + +
304A LEU* 3.9 29.4 - - + -
319A GLU* 4.1 26.7 - - - +
322A TRP* 4.3 8.7 - - + -
323A PHE 4.8 0.9 - - - +
341A LEU* 4.2 5.4 - - + -
342A ILE 3.2 12.6 - - - +
343A ARG* 4.0 16.6 - - + -
346A GLY 3.9 1.2 + - - -
347A ILE* 1.3 76.1 - - - +
349A LEU* 1.3 62.7 - - - +
350A LEU* 4.0 28.5 - - + -
383A VAL* 4.5 0.4 - - - -
398A ASN* 2.9 5.8 + - - -
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A CYS 4.5 0.9 - - - -
299A VAL 3.3 32.3 - - - +
300A GLY* 3.8 7.9 - - - +
341A LEU* 3.6 3.1 - - - -
342A ILE* 2.9 35.6 + - + -
348A MET* 1.3 74.8 - - - +
350A LEU* 1.3 66.6 + - - +
383A VAL* 3.9 16.8 - - + +
384A ALA* 4.5 0.4 - - - -
385A ILE* 3.8 23.5 - - + +
396A VAL* 3.4 48.7 - - + +
398A ASN* 4.0 17.0 - - + +
445A LEU* 4.4 3.6 - - + -
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Residues in contact with LEU 350 (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 TYR 3.4 3.7 - - - +
298A CYS* 3.5 2.8 - - - -
299A VAL* 2.9 38.9 + - + +
301A PHE* 4.3 3.4 - - + -
323A PHE* 4.0 15.5 - - + -
326A VAL* 4.0 24.9 - - + -
338A LYS* 5.8 0.9 - - + -
340A LYS 3.6 2.7 - - - +
341A LEU* 3.5 41.3 - - + -
348A MET* 4.0 24.5 - - + -
349A LEU* 1.3 78.1 - - - +
351A LEU* 1.3 60.1 + - - +
352A TYR* 3.8 33.4 - - + +
385A ILE* 4.3 2.0 - - - -
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Residues in contact with LEU 351 (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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296A VAL* 3.6 30.7 - - + -
297A TYR 3.3 6.3 - - - +
298A CYS* 4.1 11.7 - - + -
338A LYS* 3.7 3.5 - - - +
339A VAL* 2.7 61.5 + - + -
340A LYS 2.9 13.1 + - - +
349A LEU* 6.0 0.2 - - + -
350A LEU* 1.3 74.4 - - - +
352A TYR* 1.3 55.6 + - - +
353A VAL* 5.0 2.0 - - + -
385A ILE* 3.8 28.0 - - + +
387A PHE* 3.6 42.2 - - + -
396A VAL* 5.4 1.6 - - + -
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Residues in contact with TYR 352 (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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296A VAL* 3.4 4.7 - - - +
297A TYR* 2.7 54.7 + - + +
299A VAL* 5.0 1.8 - - + -
323A PHE* 3.0 33.4 + + - -
326A VAL* 3.5 32.4 - - + +
327A SER* 2.8 30.1 + - - -
330A LEU* 3.6 23.1 - - + -
336A TYR* 4.3 14.8 - - + -
337A ALA 3.2 9.0 - - - +
338A LYS* 3.8 22.4 - - + -
339A VAL 4.3 0.4 - - - +
350A LEU* 3.8 19.0 - - + +
351A LEU* 1.3 76.5 - - - +
353A VAL* 1.3 65.0 + - - +
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Residues in contact with VAL 353 (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 ASP 3.3 8.7 - - - +
296A VAL* 4.1 21.1 - - + -
336A TYR* 3.4 6.1 - - - -
337A ALA* 2.8 29.9 + - + +
339A VAL* 3.6 21.5 - - + -
351A LEU* 5.0 2.9 - - + -
352A TYR* 1.3 79.5 - - - +
354A LYS* 1.3 73.0 + - - +
357A HIS* 4.2 7.9 - - + -
358A ALA* 4.0 24.9 - - + +
361A ILE* 3.8 27.6 - - + -
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Residues in contact with LYS 354 (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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293A ALA* 3.8 19.5 + - - +
294A PRO 3.5 26.0 - - - +
295A ASP* 2.9 37.7 + - - +
334A ALA* 3.9 23.8 - - + -
335A LYS 3.4 8.5 - - - +
336A TYR* 3.7 10.2 - - + -
353A VAL* 1.3 75.8 - - - +
355A GLN* 1.3 67.3 + - - +
356A GLU* 4.2 23.2 + - + +
357A HIS* 2.8 27.3 + - + +
358A ALA 3.5 5.7 + - - -
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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