Contacts of the helix formed by residues 378 - 391 (chain A) in PDB entry 3RAW
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 GLU 378 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A ARG* 3.7 10.7 - - - +
376A THR* 3.2 6.7 + - - -
377A HIS* 1.3 93.5 - - + +
379A ASN* 1.3 70.4 + - - +
380A ARG* 2.9 27.7 + - - +
381A GLU* 2.8 33.8 + - - +
382A HIS* 3.1 18.2 + - - +
406A TYR* 4.7 4.3 + - - -
420A ASP* 4.2 14.0 - - - +
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Residues in contact with ASN 379 (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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334A ILE* 6.1 3.0 - - - +
338A ARG* 2.9 22.4 + - - +
341A ARG* 4.4 4.9 + - - -
346A ILE* 3.8 32.2 + - + +
378A GLU* 1.3 79.3 + - - +
380A ARG* 1.3 58.8 + - - +
382A HIS* 3.2 8.2 + - - +
383A LEU* 3.0 33.1 + - - +
406A TYR* 3.1 30.7 + - + +
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Residues in contact with ARG 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 2.9 22.2 + - - +
379A ASN* 1.3 70.1 - - - +
381A GLU* 1.3 67.0 + - - +
383A LEU* 3.2 7.2 + - - +
384A VAL* 3.0 27.5 + - + +
405A LYS* 3.0 42.2 + - - +
406A TYR* 3.6 36.0 - - + +
412A LEU* 4.7 3.1 - - + +
413A VAL* 3.1 44.9 + - - +
414A TRP* 4.1 16.8 - - + +
415A ASP 5.2 1.1 - - - +
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Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLN 4.8 0.9 - - - +
376A THR* 2.4 26.0 + - - -
377A HIS* 2.9 22.9 + - - -
378A GLU* 2.8 18.7 + - - +
380A ARG* 1.3 76.3 - - - +
382A HIS* 1.3 61.8 + - - +
384A VAL* 3.3 11.2 + - - +
385A MET* 3.0 40.4 + - + +
420A ASP* 3.3 44.2 - - + +
423A TYR* 4.5 6.9 - - - +
424A VAL* 3.6 21.3 - - + +
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Residues in contact with HIS 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG* 3.1 35.2 + - - +
341A ARG* 3.4 20.9 + - + -
346A ILE* 3.4 19.2 - - + +
374A PHE* 3.5 32.0 - + + +
376A THR* 3.5 28.3 + - + +
378A GLU 3.1 14.7 + - - +
379A ASN* 3.2 12.2 + - - +
381A GLU* 1.3 76.3 - - - +
383A LEU* 1.3 57.1 + - - +
385A MET* 3.2 4.5 + - - +
386A MET* 3.0 41.8 + - + +
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PRO* 4.7 5.2 - - + -
346A ILE* 4.2 17.9 - - + -
347A LEU* 4.1 26.2 - - + -
379A ASN 3.0 20.5 + - - +
380A ARG* 3.2 5.6 + - - +
382A HIS* 1.3 73.1 - - - +
384A VAL* 1.3 61.0 + - - +
386A MET* 3.3 22.4 + - - +
387A GLU* 3.0 26.7 + - - +
393A ILE* 4.0 18.3 - - + +
406A TYR* 3.7 40.8 - - + -
407A PHE* 4.8 0.7 - - + -
412A LEU* 3.5 25.4 - - + +
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ARG* 3.0 17.5 + - + +
381A GLU* 3.5 10.5 - - - +
383A LEU* 1.3 75.7 - - - +
385A MET* 1.3 56.7 + - - +
387A GLU* 3.2 4.4 + - + +
388A LYS* 2.9 32.4 + - + +
412A LEU* 3.4 13.4 - - + +
414A TRP* 3.4 67.3 - - + +
424A VAL* 3.7 19.7 - - + -
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Residues in contact with MET 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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373A LEU 5.0 0.7 - - - +
374A PHE* 3.8 20.9 - - + -
375A GLN 3.6 36.8 - - - +
376A THR* 3.8 19.1 - - - -
381A GLU* 3.0 30.2 + - + +
382A HIS* 3.2 6.3 + - - +
384A VAL* 1.3 72.0 - - - +
386A MET* 1.3 62.2 + - - +
388A LYS* 3.1 3.5 + - - +
389A ILE* 2.7 35.5 + - + +
423A TYR* 3.8 17.0 - - + -
424A VAL* 3.7 28.7 - - + -
428A CYS* 3.6 23.8 - - - -
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Residues in contact with MET 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ARG 3.7 12.1 - - - +
343A PRO* 3.9 32.1 - - + -
346A ILE* 3.7 21.3 - - + -
358A TRP* 3.9 11.7 - - + -
374A PHE* 3.8 24.5 - - + -
382A HIS* 3.0 42.1 + - + +
383A LEU* 3.3 15.9 + - - +
385A MET* 1.3 78.4 - - - +
387A GLU* 1.3 56.8 + - - +
389A ILE* 4.8 0.2 - - - -
390A LEU* 2.8 36.2 + - + +
391A GLY 3.7 0.2 + - - -
455A PHE* 3.7 22.9 - - + -
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Residues in contact with GLU 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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383A LEU 3.0 10.0 + - - +
384A VAL* 3.7 9.6 - - + +
385A MET 3.1 0.4 - - - -
386A MET* 1.3 76.3 - - - +
388A LYS* 1.3 61.8 + - + +
391A GLY* 2.7 42.8 + - - +
392A PRO* 3.4 14.3 - - - +
393A ILE* 3.0 48.0 + - + +
398A ILE* 5.4 2.9 - - - +
407A PHE* 5.6 0.2 - - - -
411A GLY* 5.9 0.2 - - - -
412A LEU* 4.1 23.2 + - + +
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Residues in contact with LYS 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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384A VAL* 2.9 22.0 + - + +
385A MET* 3.1 3.6 + - - +
387A GLU* 1.3 78.6 - - + +
389A ILE* 1.3 59.5 + - - +
414A TRP* 3.7 37.1 - - - -
424A VAL* 4.1 15.3 - - + +
425A LYS* 4.5 13.5 - - - +
428A CYS* 4.1 26.2 - - + +
429A LYS* 3.6 1.9 - - - -
430A PRO* 3.6 21.7 - - - +
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Residues in contact with ILE 389 (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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373A LEU* 3.8 39.7 - - + +
374A PHE* 3.5 27.8 - - + -
385A MET* 2.7 25.3 + - + +
388A LYS* 1.3 76.0 - - - +
390A LEU* 1.3 73.4 + - + +
391A GLY 3.8 0.2 - - - -
428A CYS* 4.1 16.8 - - + -
429A LYS 3.4 17.0 - - - +
430A PRO* 3.5 3.2 - - - +
431A LEU* 2.8 49.4 + - + +
434A TYR* 4.8 4.9 - - + +
450A ARG* 4.7 2.4 + - - -
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A TRP* 3.6 32.1 - - + -
374A PHE* 4.1 15.0 - - + -
386A MET* 2.8 17.8 + - - +
389A ILE* 1.3 92.9 - - + +
391A GLY* 1.3 57.9 + - - +
431A LEU* 4.0 19.1 - - + -
450A ARG* 4.6 19.3 + - + +
453A LEU* 3.8 39.3 - - + +
455A PHE* 4.0 17.3 - - + -
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Residues in contact with GLY 391 (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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387A GLU* 2.7 36.7 + - - -
388A LYS 4.7 0.2 - - - -
389A ILE 3.8 0.6 - - - -
390A LEU* 1.3 73.2 - - - +
392A PRO* 1.3 79.0 - - - +
455A PHE* 3.1 15.2 - - - -
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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