Contacts of the helix formed by residues 397 - 407 (chain A) in PDB entry 1R6U
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 ASP 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A PHE 3.7 2.1 - - - +
378A SER* 3.3 9.4 + - - -
379A GLY* 3.0 27.3 + - - +
393A ASN 3.3 17.5 + - - +
394A CYS 3.3 5.2 + - - +
396A VAL* 1.3 75.0 - - - +
398A VAL* 1.3 65.7 + - - +
399A SER* 2.8 19.5 + - - -
400A PHE* 2.7 33.0 + - + +
401A MSE 3.0 23.9 + - - +
420A TYR* 3.1 27.7 + - + -
427A THR* 5.0 1.6 - - - +
430A LEU* 4.1 2.7 - - - +
431A LYS* 5.3 1.2 - - - -
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Residues in contact with VAL 398 (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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341A PRO* 4.7 4.7 - - + -
342A ALA 3.6 11.0 - - - +
343A LEU* 3.5 26.9 - - - +
345A GLY* 3.9 12.8 - - - -
346A ALA 4.5 2.2 - - - +
376A ALA* 4.6 6.7 - - + -
377A PHE* 3.3 27.6 + - + +
396A VAL 3.3 4.9 + - - +
397A ASP* 1.3 72.0 - - - +
399A SER* 1.3 58.1 + - - +
401A MSE 3.2 8.7 + - - +
402A TYR* 2.9 65.3 + - + +
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Residues in contact with SER 399 (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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372A VAL* 3.8 0.2 - - - +
376A ALA* 3.7 14.8 - - - +
377A PHE 4.1 1.4 + - - -
397A ASP* 2.8 20.6 + - - -
398A VAL* 1.3 75.9 - - - +
400A PHE* 1.3 59.4 + - - -
402A TYR* 3.3 3.6 + - - +
403A LEU* 3.2 25.2 + - - +
430A LEU* 4.6 11.2 - - - -
431A LYS* 3.7 31.2 - - - +
434A LEU* 3.6 25.3 - - - +
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Residues in contact with PHE 400 (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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394A CYS* 3.5 42.6 - - + +
397A ASP* 2.7 24.7 + - + +
399A SER* 1.3 70.0 - - - +
401A MSE 1.3 69.5 + - + +
403A LEU* 2.9 22.8 + - + +
404A THR* 3.1 33.3 + - + +
413A LEU* 3.9 24.5 - - + -
416A ILE* 4.5 14.1 - - + -
417A ARG* 3.5 41.3 - - + -
420A TYR* 5.8 0.4 - - + -
430A LEU* 4.6 9.1 - - + +
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Residues in contact with MSE 401 (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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96A LYS 4.0 20.6 - - - +
341A PRO* 3.9 33.9 - - + -
346A ALA* 4.0 13.7 - - + -
394A CYS 4.1 7.0 - - - +
395A ASP* 2.8 31.4 - - - +
396A VAL 4.4 4.5 - - - +
397A ASP 3.0 20.9 + - - +
398A VAL* 3.5 10.5 - - - +
400A PHE* 1.3 78.1 - - + +
402A TYR* 1.3 64.1 + - + +
404A THR* 2.6 29.7 + - - -
405A PHE* 3.1 12.3 - - + -
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Residues in contact with TYR 402 (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 PHE* 3.6 39.9 - + + -
341A PRO* 3.0 33.3 + - + -
343A LEU* 3.4 21.6 + - + +
350A MSE 3.0 14.4 - - - +
359A ILE* 3.9 21.8 - - + -
372A VAL* 6.3 0.2 - - + -
376A ALA* 6.0 0.4 - - + -
398A VAL* 2.9 37.8 + - + -
399A SER 3.6 4.3 - - - +
400A PHE 3.2 0.2 - - - -
401A MSE 1.3 78.8 - - + +
403A LEU* 1.3 62.3 + - - +
405A PHE* 3.1 7.3 + - - +
406A PHE* 3.1 24.5 + - + +
434A LEU* 3.5 34.3 - - + -
438A LEU* 4.3 11.2 - - + -
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Residues in contact with LEU 403 (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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134A ARG* 3.8 1.4 + - - -
399A SER 3.2 14.1 + - - +
400A PHE* 2.9 15.1 + - + +
402A TYR* 1.3 74.9 - - - +
404A THR* 1.3 59.1 + - - +
405A PHE 3.0 5.2 - - - -
406A PHE* 5.1 0.2 - - - +
407A LEU* 2.7 44.2 + - + +
413A LEU* 3.8 13.2 - - + +
416A ILE* 4.1 23.1 - - + -
430A LEU* 3.9 33.4 - - + +
433A ALA* 4.4 3.6 - - + -
434A LEU* 3.6 32.1 - - + +
437A VAL* 3.9 20.4 - - + -
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Residues in contact with THR 404 (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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130A HIS* 4.3 2.9 + - - -
134A ARG* 2.9 30.5 + - - -
136A ILE* 4.3 15.9 - - - +
400A PHE* 3.1 41.6 + - + +
401A MSE 2.6 21.3 + - - +
403A LEU* 1.3 75.8 - - - +
405A PHE* 1.3 65.4 + - - +
413A LEU* 3.8 19.3 - - + -
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Residues in contact with PHE 405 (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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130A HIS* 3.1 23.1 - - - -
131A PHE* 3.3 15.4 - + - -
136A ILE* 3.3 36.3 - - + -
175A ILE* 3.7 29.4 - - + -
338A THR* 3.7 19.7 - - - -
339A PHE 4.1 13.0 - - - -
340A PHE* 3.8 23.1 - + - -
341A PRO* 4.1 13.2 - - + -
401A MSE 3.1 28.0 - - + -
402A TYR 3.1 6.9 + - - +
403A LEU 3.0 0.2 - - - -
404A THR* 1.3 90.1 + - - +
406A PHE* 1.3 78.5 + - + +
407A LEU 3.9 0.2 - - - -
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Residues in contact with PHE 406 (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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130A HIS* 4.6 4.4 - + - -
131A PHE* 5.5 0.4 - + - -
171A VAL* 3.3 31.4 - - + -
174A LEU* 4.7 2.2 - - + -
175A ILE* 3.7 21.3 - - + -
178A ILE* 3.8 26.5 - - + -
340A PHE* 3.3 26.9 - + - -
402A TYR 3.1 18.1 + - - +
403A LEU* 5.3 0.4 - - - -
405A PHE* 1.3 84.2 - - + +
407A LEU* 1.3 60.1 + - - +
408A GLU* 3.2 8.6 + - - +
434A LEU* 5.9 0.7 - - + -
437A VAL* 3.7 27.3 - - + +
438A LEU* 4.0 15.3 - - + -
441A LEU* 3.5 27.4 - - + -
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Residues in contact with LEU 407 (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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130A HIS* 5.1 0.2 - - - -
134A ARG* 2.6 39.6 + - - -
403A LEU* 2.7 36.9 + - + +
406A PHE* 1.3 71.1 - - - +
408A GLU* 1.3 52.7 + - - +
409A ASP* 4.1 10.3 - - + +
412A LYS* 4.0 24.7 - - + -
413A LEU* 3.7 31.0 - - + +
416A ILE* 3.7 30.3 - - + -
437A VAL* 4.0 21.3 - - + +
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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