Contacts of the helix formed by residues 411 - 425 (chain A) in PDB entry 2P6U
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 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A GLU* 5.6 11.0 - - + +
408A LYS* 3.6 13.6 + - + +
409A LEU 3.4 2.8 + - - +
410A GLY* 1.3 78.2 - - - +
412A GLU* 1.3 71.7 + - + +
413A THR* 3.2 30.5 + - - +
414A HIS* 3.7 12.9 + - + +
415A LEU* 2.9 18.7 + - - +
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Residues in contact with GLU 412 (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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410A GLY 3.6 1.0 + - - -
411A VAL* 1.3 73.2 - - + +
413A THR* 1.3 73.0 - - - +
415A LEU* 2.8 16.4 + - + +
416A ARG* 2.8 27.5 + - + +
454A GLU* 5.4 5.4 - - + -
457A ARG* 3.4 32.7 + - - +
458A VAL* 4.7 5.9 - - + +
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Residues in contact with THR 413 (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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411A VAL* 3.2 19.2 - - - +
412A GLU* 1.3 80.6 - - - +
414A HIS* 1.3 69.6 + - + +
416A ARG* 2.9 28.6 + - - +
417A PHE* 2.8 33.2 + - + +
489A ASP* 4.7 9.3 - - - +
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Residues in contact with HIS 414 (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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153A GLU* 3.0 30.8 + - + -
154A LYS* 4.9 6.7 + - - -
157A ALA* 3.4 34.7 - - + +
408A LYS* 3.6 21.4 + - + -
409A LEU* 4.0 12.8 - - + +
411A VAL* 3.7 12.6 + - + +
412A GLU 3.4 0.4 - - - -
413A THR* 1.3 98.8 - - + +
415A LEU* 1.3 57.6 + - - +
417A PHE* 4.1 5.2 - - + -
418A HIS* 2.8 44.0 + + + +
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Residues in contact with LEU 415 (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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409A LEU 3.5 14.1 - - - +
410A GLY 3.2 18.4 - - - +
411A VAL 2.9 16.4 - - - +
412A GLU* 2.8 17.9 + - + +
414A HIS* 1.3 76.2 - - - +
416A ARG* 1.3 50.5 + - - +
418A HIS* 4.0 0.2 - - - -
419A SER* 2.2 45.0 + - - -
438A PHE* 3.2 36.4 - - + -
451A LEU* 4.0 10.1 - - + -
454A GLU* 4.1 29.6 - - + -
455A LEU* 3.9 14.4 - - + +
458A VAL* 4.2 9.9 - - + -
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Residues in contact with ARG 416 (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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412A GLU* 2.8 17.4 + - + +
413A THR* 3.2 26.9 + - - +
415A LEU* 1.3 75.6 - - - +
417A PHE* 1.3 64.1 + - - +
419A SER* 3.8 0.5 - - - -
420A LEU* 3.2 22.5 + - - +
458A VAL* 3.9 19.9 - - + +
461A GLN* 3.4 28.8 + - - +
462A LEU* 3.7 22.8 - - + +
465A TRP* 3.9 20.5 - - - -
489A ASP* 3.4 33.1 + - - -
490A PRO* 3.9 6.4 - - + +
491A LEU* 3.9 18.8 - - - +
518A PRO* 6.0 0.4 - - - +
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Residues in contact with PHE 417 (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 ARG* 3.4 40.1 + - - -
413A THR* 2.8 15.0 + - + +
414A HIS* 3.3 12.5 + - + +
416A ARG* 1.3 80.0 - - - +
418A HIS* 1.3 83.9 + + - +
420A LEU* 3.9 5.4 - - - +
421A SER* 3.8 12.0 + - - -
487A TYR* 3.7 34.8 - + - -
488A ILE 3.9 22.0 - - - -
489A ASP* 3.9 22.9 - - + +
490A PRO* 3.9 13.2 - - + +
519A ASP* 5.7 1.6 - - - -
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Residues in contact with HIS 418 (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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126A ASP* 4.2 6.2 + - - -
130A ARG* 4.5 1.8 + - - -
157A ALA* 3.8 18.5 - - + +
158A THR* 3.9 32.5 + - + -
161A ILE* 3.5 43.7 - - + +
409A LEU* 4.5 2.2 - - + -
414A HIS* 2.8 43.9 + - + +
415A LEU 4.2 0.7 - - - +
417A PHE* 1.3 96.5 - + - +
419A SER* 1.3 66.9 + - - +
421A SER* 2.9 9.6 + - - -
422A ILE* 2.8 25.9 + - + +
438A PHE* 4.5 5.8 - - + -
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Residues in contact with SER 419 (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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415A LEU 2.2 36.6 + - - -
416A ARG 3.8 0.4 - - - -
418A HIS* 1.3 71.0 - - - +
420A LEU* 1.3 65.7 + - - +
422A ILE* 2.7 15.0 + - - +
423A ILE* 2.7 30.3 + - - +
434A LEU* 4.4 16.8 - - - -
438A PHE* 4.1 10.6 - - - -
455A LEU* 4.4 6.8 - - - +
458A VAL* 3.7 25.0 - - - +
462A LEU* 4.4 2.5 - - - -
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Residues in contact with LEU 420 (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 ARG* 6.0 1.8 - - - +
416A ARG 3.2 13.8 + - - +
417A PHE 3.9 4.7 - - - +
419A SER* 1.3 77.1 - - - +
421A SER* 1.3 62.7 + - - +
423A ILE* 3.5 3.8 + - - +
424A CYS* 2.9 50.7 + - - -
462A LEU* 3.7 17.1 - - + +
467A MET* 4.2 14.1 - - + +
468A VAL* 4.6 9.9 - - + -
480A GLY* 3.9 16.8 - - - +
483A VAL* 3.9 23.1 - - + -
484A SER* 4.6 7.0 - - - +
488A ILE 5.4 0.7 - - - +
490A PRO* 3.3 34.5 - - + -
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Residues in contact with SER 421 (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 ARG* 3.5 35.3 + - - +
161A ILE* 5.7 0.6 - - - +
165A LYS* 2.8 32.1 + - - +
417A PHE 3.8 2.1 + - - -
418A HIS* 2.9 14.8 + - - -
420A LEU* 1.3 82.1 - - - +
422A ILE* 1.3 58.1 + - - +
424A CYS* 3.2 0.7 + - - +
425A ASP* 2.8 33.7 + - - +
484A SER* 4.1 11.7 - - - -
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Residues in contact with ILE 422 (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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161A ILE* 4.7 4.7 - - + -
165A LYS* 5.3 2.0 - - + -
418A HIS* 2.8 27.6 + - + +
419A SER* 2.7 12.2 + - - +
421A SER* 1.3 76.1 - - - +
423A ILE* 1.3 62.3 + - - +
424A CYS 3.2 0.9 + - - -
425A ASP 3.6 0.2 + - - -
426A GLY 3.4 2.3 + - - -
427A TYR* 3.2 54.5 + - + +
428A ALA* 3.6 19.3 + - + +
434A LEU* 4.2 4.3 - - + -
437A PHE* 3.4 36.1 - - + -
438A PHE* 3.4 35.4 - - + -
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Residues in contact with ILE 423 (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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419A SER* 2.7 27.8 + - - +
420A LEU* 4.0 2.9 - - - +
422A ILE* 1.3 72.3 - - - +
424A CYS* 1.3 61.7 + - - +
426A GLY* 4.0 4.9 + - - -
428A ALA* 3.6 18.6 - - + +
434A LEU* 4.4 15.7 - - + -
459A VAL* 4.1 22.7 - - + -
462A LEU* 4.0 24.2 - - + -
468A VAL* 4.1 22.7 - - + -
474A LEU* 3.8 39.8 - - + +
475A ALA* 4.4 2.9 - - - +
476A PRO* 3.9 10.5 - - + +
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Residues in contact with CYS 424 (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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420A LEU* 2.9 48.0 + - - +
421A SER 3.7 2.5 - - - +
422A ILE 3.1 0.2 - - - -
423A ILE* 1.3 77.3 - - - +
425A ASP* 1.3 65.2 + - - +
426A GLY* 2.9 11.1 + - - -
468A VAL* 6.1 0.4 - - - -
476A PRO* 3.4 38.0 - - + +
480A GLY 4.0 13.5 - - - -
481A SER* 4.3 3.8 - - - -
484A SER* 4.1 11.4 - - - +
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Residues in contact with ASP 425 (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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129A ILE* 4.1 4.2 - - - +
130A ARG* 3.1 51.7 + - - +
132A ARG* 6.1 1.3 - - - -
165A LYS* 3.4 12.6 + - - -
421A SER 2.8 23.2 + - - +
424A CYS* 1.3 73.3 - - - +
426A GLY* 1.3 60.2 + - - +
427A TYR* 3.3 26.5 + - + -
484A SER* 4.0 7.3 + - - -
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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