Contacts of the helix formed by residues 434 - 454 (chain A) in PDB entry 1R1H
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 434 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A ALA* 3.6 4.9 - - + +
433A GLY* 1.3 76.8 - - - +
435A SER* 1.3 65.8 + - - +
436A LYS 3.0 1.2 + - - -
437A HIS* 3.3 39.7 + - + +
438A VAL* 3.3 19.6 + - + +
566A ALA* 6.1 1.6 - - - -
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Residues in contact with SER 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 3.5 29.7 - - - -
432A ALA* 3.7 19.4 - - - +
434A GLU* 1.3 77.9 - - - +
436A LYS* 1.3 62.8 + - - -
438A VAL* 3.3 3.0 + - - +
439A VAL* 3.0 30.6 + - - +
559A LEU* 4.6 4.1 + - - -
564A PHE* 3.6 30.1 - - - -
566A ALA* 5.4 4.3 + - - +
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Residues in contact with LYS 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PHE* 4.2 11.7 - - + -
433A GLY 3.9 15.6 + - - +
434A GLU* 3.0 0.4 - - - +
435A SER* 1.3 80.8 - - - +
437A HIS* 1.3 63.9 + - + +
439A VAL* 3.3 1.9 + - - +
440A GLU* 2.9 54.0 + - - +
479A ILE* 3.6 42.6 - - + +
481A TYR* 4.7 20.5 + - + +
483A ASP* 4.1 20.7 + - - +
534A TRP* 6.1 0.9 - - - -
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Residues in contact with HIS 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLY 3.7 14.6 + - - -
434A GLU* 3.3 40.9 + - + +
436A LYS* 1.3 82.1 - - + +
438A VAL* 1.3 64.6 + - + +
440A GLU* 3.4 23.1 + - - +
441A ASP* 3.3 21.1 + - - +
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Residues in contact with VAL 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLU* 3.3 13.2 + - + +
435A SER 3.3 2.2 + - - +
436A LYS 3.3 0.6 - - - -
437A HIS* 1.3 76.2 - - + +
439A VAL* 1.3 64.1 + - - +
441A ASP* 3.2 8.9 + - + +
442A LEU* 3.0 29.1 + - + +
564A PHE* 3.5 32.3 - - + -
566A ALA* 4.5 20.0 - - + -
573A ASN* 6.0 0.2 - - - +
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A SER 3.0 22.4 + - - +
436A LYS 3.7 3.4 - - - +
438A VAL* 1.3 77.4 - - - +
440A GLU* 1.3 61.6 + - - +
442A LEU* 3.1 9.5 + - + +
443A ILE* 2.9 42.0 + - + +
479A ILE* 3.9 16.8 - - + -
554A PHE* 5.0 4.3 - - + -
559A LEU* 4.1 29.8 - - + -
564A PHE* 3.9 29.6 - - + -
577A ILE* 5.3 2.2 - - + -
581A ILE* 4.9 8.3 - - + -
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Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LYS* 2.9 42.1 + - - +
437A HIS* 3.4 28.8 - - - +
439A VAL* 1.3 75.6 - - - +
441A ASP* 1.3 58.1 + - - +
443A ILE* 3.5 3.4 + - - +
444A ALA* 3.1 26.0 + - - +
477A GLU* 4.0 11.8 - - - +
479A ILE* 3.1 30.2 - - + +
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Residues in contact with ASP 441 (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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437A HIS 3.3 9.1 + - - +
438A VAL* 3.2 10.8 + - - +
439A VAL 3.2 0.2 - - - -
440A GLU* 1.3 79.6 - - - +
442A LEU* 1.3 65.6 + - - +
444A ALA* 3.4 10.4 + - - +
445A GLN* 2.7 48.3 + - - +
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Residues in contact with LEU 442 (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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438A VAL* 3.0 22.7 + - + +
439A VAL* 3.1 9.6 + - - +
441A ASP* 1.3 75.7 - - - +
443A ILE* 1.3 56.2 + - - +
445A GLN* 3.1 14.4 + - - +
446A ILE* 3.0 37.2 + - + +
564A PHE* 4.1 20.9 - - + -
573A ASN* 4.7 9.4 - - + +
574A TYR* 3.7 38.6 - - + +
577A ILE* 3.8 29.2 - - + -
578A GLY* 5.4 2.0 - - - +
581A ILE* 4.1 10.5 - - + -
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Residues in contact with ILE 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 2.9 26.7 + - + +
440A GLU 3.7 3.8 - - - +
442A LEU* 1.3 73.2 - - - +
444A ALA* 1.3 65.8 + - - +
446A ILE* 3.2 1.0 + - - +
447A ARG* 3.0 32.9 + - + +
477A GLU* 3.8 19.1 - - + +
479A ILE* 3.6 32.5 - - + -
552A ILE* 3.9 21.8 - - + -
554A PHE* 3.6 21.3 - - + -
581A ILE* 3.7 31.4 - - + -
585A ILE* 4.8 2.4 - - + +
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Residues in contact with ALA 444 (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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440A GLU 3.1 13.8 + - - +
441A ASP* 3.4 15.9 - - - +
443A ILE* 1.3 78.3 - - - +
445A GLN* 1.3 60.9 + - + +
447A ARG* 3.6 12.7 + - - +
448A GLU* 3.2 23.4 + - - +
477A GLU* 4.9 2.4 + - - +
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Residues in contact with GLN 445 (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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441A ASP* 2.7 46.9 + - - +
442A LEU* 3.1 19.4 + - - +
444A ALA* 1.3 77.4 - - + +
446A ILE* 1.3 61.4 + - + +
448A GLU* 3.1 8.8 + - - +
449A VAL* 3.0 31.8 + - + +
574A TYR* 2.5 34.6 + - + -
660A ALA* 4.5 11.1 - - + +
664A TYR* 5.1 2.3 - - - +
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Residues in contact with ILE 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LEU* 3.0 28.3 + - + +
443A ILE 3.2 0.4 + - - +
445A GLN* 1.3 76.6 - - + +
447A ARG* 1.3 57.3 + - - +
449A VAL* 3.2 8.1 + - - +
450A PHE* 2.9 28.9 + - + +
574A TYR* 5.2 5.6 - - + -
578A GLY* 3.8 20.2 - - - +
581A ILE* 3.7 33.4 - - + -
582A GLY* 3.8 28.5 - - - -
585A ILE* 3.8 11.0 - - + -
656A GLN* 4.4 13.3 - - + +
657A ALA* 4.8 6.3 - - - -
660A ALA* 4.2 18.6 - - + -
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Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ILE* 3.0 24.5 + - + +
444A ALA* 3.7 10.3 - - - +
446A ILE* 1.3 78.3 - - - +
448A GLU* 1.3 61.0 + - - +
450A PHE* 3.5 6.4 + - + +
451A ILE* 3.1 36.2 + - + +
472A ALA* 2.6 44.4 + - + +
473A LEU* 3.5 16.7 + - - +
475A ILE* 2.9 38.2 + - + +
477A GLU* 3.5 32.1 + - - +
552A ILE* 5.5 0.9 - - - +
585A ILE* 4.1 17.6 - - + +
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Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ALA 3.2 10.9 + - - +
445A GLN* 3.1 12.9 + - - +
447A ARG* 1.3 78.7 - - - +
449A VAL* 1.3 60.0 + - + +
451A ILE* 3.3 27.5 + - - +
452A GLN* 2.8 70.3 + - - +
473A LEU* 5.2 1.7 - - - +
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Residues in contact with VAL 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLN* 3.0 18.2 + - + +
446A ILE* 3.2 8.2 + - - +
448A GLU* 1.3 76.1 - - + +
450A PHE* 1.3 56.8 + - - +
452A GLN* 3.4 9.3 + - + +
453A THR* 2.7 44.4 + - - +
656A GLN* 3.6 29.4 - - + +
659A ARG* 3.7 18.4 - - + -
660A ALA* 3.9 26.5 - - + -
663A ASN* 4.0 17.3 - - - +
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Residues in contact with PHE 450 (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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446A ILE* 2.9 12.9 + - + +
447A ARG* 3.6 11.0 - - - +
449A VAL* 1.3 74.4 - - - +
451A ILE* 1.3 69.7 + - - +
453A THR* 3.1 16.1 + - - -
454A LEU* 3.3 29.3 + - + +
468A ALA 4.5 0.9 - - - -
472A ALA* 4.1 17.9 - - + -
585A ILE* 4.3 17.3 - - + -
586A THR* 4.7 3.4 - - - -
589A PHE* 3.5 54.1 - + + -
656A GLN* 3.4 31.6 - - + +
749A TRP* 4.0 33.9 - + + -
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Residues in contact with ILE 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ARG* 3.1 24.7 + - + +
448A GLU* 3.4 30.7 - - - +
450A PHE* 1.3 79.6 - - - +
452A GLN* 1.3 68.7 + - + +
454A LEU* 3.1 28.4 + - - +
455A ASP* 3.8 4.3 - - - +
469A GLU* 4.4 29.5 - - + +
472A ALA* 3.7 23.8 - - + -
473A LEU* 3.6 32.8 - - + -
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Residues in contact with GLN 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A GLU* 2.8 54.5 + - - +
449A VAL* 3.8 7.3 - - - +
451A ILE* 1.3 76.0 - - + +
453A THR* 1.3 62.7 + - - +
454A LEU 3.3 0.7 + - - -
455A ASP* 3.3 23.1 + - - +
456A ASP* 3.8 6.3 - - - +
663A ASN* 4.7 11.8 + - - -
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Residues in contact with THR 453 (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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449A VAL* 2.7 24.1 + - - +
450A PHE* 3.5 8.5 - - - -
451A ILE 3.1 0.4 - - - -
452A GLN* 1.3 72.1 - - - +
454A LEU* 1.3 64.0 + - - +
455A ASP 2.8 8.0 + - - -
456A ASP* 2.9 25.5 + - + +
457A LEU* 3.4 16.4 + - + +
656A GLN* 5.9 1.6 - - + -
659A ARG* 3.6 26.3 + - - +
747A ARG* 3.5 27.6 - - - +
749A TRP 4.0 10.8 - - - +
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Residues in contact with LEU 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A PHE* 3.3 23.9 + - + +
451A ILE* 3.1 21.5 + - - +
453A THR* 1.3 78.1 - - - +
455A ASP* 1.3 62.1 + - - +
457A LEU* 3.3 14.6 + - + +
460A MET* 5.1 3.6 - - - -
465A LYS* 2.8 51.1 + - + +
468A ALA* 3.9 8.7 - - + -
469A GLU* 3.7 37.5 - - + +
749A TRP* 3.8 31.9 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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