Contacts of the helix formed by residues 445 - 463 (chain A) in PDB entry 1UOR
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 ARG 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A ILE* 3.3 37.2 + - + +
392A CYS* 4.6 10.8 - - - +
396A GLU* 5.9 0.8 + - - -
437A CYS 3.1 21.9 + - - +
438A CYS* 3.1 18.0 + - - +
440A HIS* 3.6 10.0 - - - -
441A PRO* 2.9 48.6 + - - +
442A GLU 3.8 14.0 + - - +
443A ALA 2.4 12.2 + - - +
444A LYS* 1.3 68.7 - - - +
446A MET* 1.3 70.8 + - - +
448A CYS* 3.0 18.9 + - - -
449A ALA* 3.2 12.2 + - + +
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Residues in contact with MET 446 (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 ASP 4.4 7.2 - - - +
341A TYR* 4.1 15.0 - - + -
342A SER* 3.0 38.5 - - - +
345A LEU* 3.8 18.4 - - + -
381A VAL* 5.6 1.8 - - + +
384A PRO* 3.0 39.3 - - + -
385A GLN* 4.1 12.8 - - + +
388A ILE* 5.2 10.3 - - + -
442A GLU 4.8 0.2 + - - -
443A ALA 2.9 8.6 + - - +
445A ARG* 1.3 80.2 - - + +
447A PRO* 1.3 73.7 - - + +
449A ALA* 2.7 16.7 + - - +
450A GLU* 3.2 14.2 + - + +
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Residues in contact with PRO 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLN* 5.8 6.3 - - - -
222A ARG* 6.3 1.3 - - - +
339A PRO 3.2 28.9 - - - +
340A ASP 4.5 6.7 - - - +
341A TYR 4.6 2.9 - - - +
342A SER* 4.0 16.7 - - - -
443A ALA 2.9 28.7 - - - +
444A LYS* 3.5 9.9 - - - +
445A ARG 3.4 3.6 - - - -
446A MET* 1.3 79.2 - - + +
448A CYS* 1.3 56.0 + - - +
451A ASP* 2.5 34.3 - - - +
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Residues in contact with CYS 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A VAL* 5.5 0.2 - - - -
436A LYS* 5.0 7.2 - - - +
437A CYS* 2.0 52.7 - - - -
440A HIS* 5.0 2.5 - - + +
444A LYS 3.9 9.1 + - - +
445A ARG 3.0 8.8 + - - +
446A MET 2.7 4.0 + - - -
447A PRO* 1.3 77.3 - - - +
449A ALA* 1.3 65.3 + - - +
450A GLU 3.7 0.2 - - - -
451A ASP* 3.4 4.1 - - - +
452A TYR* 2.6 39.4 + - + +
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ILE* 4.3 22.7 - - + +
433A VAL* 4.5 12.3 - - + +
437A CYS* 4.3 8.7 - - + -
445A ARG* 3.7 13.0 - - + +
446A MET* 2.7 11.4 + - - +
448A CYS* 1.3 87.9 - - - +
450A GLU* 1.3 60.5 + - - +
452A TYR* 4.2 5.8 - - - +
453A LEU* 3.0 29.3 + - - +
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Residues in contact with GLU 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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342A SER* 2.5 37.8 + - - +
344A VAL* 3.5 23.5 - - + +
345A LEU* 3.1 29.7 + - - +
348A ARG* 5.4 2.4 - - - -
384A PRO* 4.7 11.7 - - + -
387A LEU* 6.2 0.2 - - + -
388A ILE* 5.1 3.1 - - + +
446A MET* 3.2 11.5 + - + +
449A ALA* 1.3 72.7 - - - +
451A ASP* 1.3 54.7 + - - +
453A LEU* 3.2 7.1 - - - +
454A SER* 2.3 38.9 + - - +
482A VAL 5.3 0.2 - - - +
485A ARG* 3.4 42.9 + - + +
486A PRO* 4.3 6.2 - - - +
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Residues in contact with ASP 451 (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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198A LEU* 5.7 0.3 - - - +
214A TRP* 5.7 1.6 - - - -
218A ARG* 3.7 20.4 + - - +
222A ARG* 5.7 0.7 + - - -
342A SER* 4.1 3.8 - - - -
343A VAL* 3.1 39.0 + - - +
344A VAL* 3.4 13.7 - - - +
447A PRO* 2.5 29.4 - - - +
448A CYS* 3.4 2.9 - - - +
450A GLU* 1.3 79.0 - - - +
452A TYR* 1.3 62.3 + - - +
454A SER* 2.9 8.5 + - - -
455A VAL* 3.0 25.9 + - - +
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Residues in contact with TYR 452 (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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195A LYS* 6.3 5.8 - - + -
429A ASN* 3.7 31.3 + - - -
430A LEU* 4.6 0.9 - - - -
432A LYS* 4.0 19.9 + - - +
433A VAL* 3.2 29.8 - - + -
436A LYS* 5.6 14.1 - - + -
437A CYS* 6.0 3.6 - - - -
448A CYS* 2.6 24.9 + - - +
449A ALA* 4.5 0.4 - - - -
450A GLU 3.5 0.2 - - - -
451A ASP* 1.3 67.7 - - - +
453A LEU* 1.3 68.4 + - - +
455A VAL* 2.8 26.3 + - + +
456A VAL* 3.1 30.8 + - + -
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Residues in contact with LEU 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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387A LEU* 4.4 9.2 - - + -
391A ASN* 3.6 26.9 - - - +
407A LEU* 6.4 0.4 - - + -
411A TYR* 5.2 3.6 - - - +
430A LEU* 3.7 35.2 - - + +
433A VAL* 4.2 13.7 - - + +
449A ALA 3.0 20.2 + - - +
450A GLU 3.2 9.4 + - - +
452A TYR* 1.3 79.9 - - - +
454A SER* 1.3 63.0 + - - +
456A VAL* 3.0 16.7 + - - +
457A LEU* 3.1 22.6 + - + +
485A ARG* 4.1 28.5 - - + -
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Residues in contact with SER 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 4.6 9.7 - - - +
344A VAL* 3.8 25.2 - - - +
450A GLU* 2.3 43.7 + - - +
451A ASP* 2.9 13.8 - - - -
452A TYR 2.9 0.2 + - - -
453A LEU* 1.3 74.4 - - - +
455A VAL* 1.3 59.5 + - - +
457A LEU* 3.9 10.3 + - - +
458A ASN* 3.5 17.0 + - - +
484A ARG* 4.1 14.4 - - - +
485A ARG* 5.1 6.5 - - - +
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Residues in contact with VAL 455 (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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194A ALA* 3.1 38.4 - - + +
195A LYS* 4.1 18.6 - - + +
198A LEU* 4.3 24.4 - - + +
451A ASP 3.0 15.5 + - - +
452A TYR* 2.8 20.5 + - + +
454A SER* 1.3 70.7 - - - +
456A VAL* 1.3 62.7 + - + +
458A ASN* 2.8 20.8 + - - +
459A GLN* 3.0 12.9 + - + +
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Residues in contact with VAL 456 (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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426A VAL* 3.2 36.1 - - + -
429A ASN* 4.6 9.9 - - + +
430A LEU* 3.7 26.5 - - + +
452A TYR* 3.1 37.2 + - + +
453A LEU* 3.0 7.4 + - - +
455A VAL* 1.3 74.4 - - + +
457A LEU* 1.3 69.2 + - + +
458A ASN 2.9 1.1 - - - -
459A GLN* 2.8 24.7 + - + +
460A LEU* 2.8 10.8 + - - +
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Residues in contact with LEU 457 (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 TYR* 4.7 13.2 - - + +
426A VAL* 5.0 1.6 - - + -
430A LEU* 4.1 26.0 - - + -
453A LEU* 3.1 16.9 + - + +
454A SER* 4.0 5.6 - - - +
456A VAL* 1.3 79.8 - - + +
458A ASN* 1.3 55.5 + - - +
460A LEU* 2.9 16.7 - - + +
461A CYS* 2.9 32.4 + - - -
484A ARG* 4.2 18.4 - - + -
485A ARG* 3.8 42.8 - - + +
488A PHE* 4.0 25.4 - - + -
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Residues in contact with ASN 458 (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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194A ALA 5.0 2.0 + - - -
197A ARG* 3.5 9.1 - - - +
198A LEU* 3.1 55.4 - - + +
201A ALA* 3.5 11.3 - - - +
205A LYS* 5.8 0.5 - - - -
454A SER 3.5 5.6 + - - +
455A VAL 2.8 13.3 + - - +
456A VAL 2.8 1.2 + - - -
457A LEU* 1.3 76.3 - - - +
459A GLN* 1.3 64.1 + - - +
461A CYS* 2.8 3.6 + - - +
462A VAL* 2.8 46.1 + - - +
484A ARG* 3.4 25.6 + - - +
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Residues in contact with GLN 459 (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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109A ASN* 3.0 26.6 + - - +
193A SER 5.5 0.3 - - - +
194A ALA* 3.2 35.7 + - - +
197A ARG* 5.3 5.1 - - - +
425A GLU* 5.1 12.3 + - + +
426A VAL* 5.7 4.0 - - + -
429A ASN* 5.1 7.9 + - - -
455A VAL* 3.0 10.0 + - + +
456A VAL* 2.8 21.7 + - + +
458A ASN* 1.3 70.9 - - - +
460A LEU* 1.3 63.9 + - - +
462A VAL* 3.0 8.4 - - - +
463A LEU* 2.8 44.9 + - + +
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Residues in contact with LEU 460 (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 TYR* 5.2 6.3 - - + -
415A VAL* 6.3 0.4 - - + -
418A VAL* 3.9 31.6 - - + -
422A THR* 4.7 6.7 - - + +
423A LEU* 6.4 0.2 - - + -
426A VAL* 4.4 22.6 - - + +
456A VAL 2.8 11.7 + - - +
457A LEU* 2.9 25.8 - - + +
459A GLN* 1.3 73.5 - - - +
461A CYS* 1.3 58.5 + - - +
463A LEU* 3.6 6.4 - - - +
464A HIS* 3.4 19.0 + - + +
473A VAL* 4.0 19.9 - - + +
488A PHE* 3.4 40.2 - - + -
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Residues in contact with CYS 461 (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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205A LYS* 5.6 5.2 - - - +
457A LEU 2.9 18.9 + - - -
458A ASN 2.8 13.1 + - - +
460A LEU* 1.3 73.1 - - - +
462A VAL* 1.3 62.3 + - + +
464A HIS 3.5 20.6 + - - +
465A GLU* 3.6 11.9 + - - +
473A VAL* 5.4 0.9 - - - -
477A CYS* 2.0 55.9 - - + -
484A ARG* 3.6 26.2 - - - +
488A PHE* 5.1 3.4 - - - -
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Residues in contact with VAL 462 (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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108A ASP* 3.5 30.6 - - - +
109A ASN* 4.7 5.8 - - - +
197A ARG* 3.7 39.9 - - + +
201A ALA* 4.9 1.6 - - + -
205A LYS* 5.0 6.3 - - - +
458A ASN* 2.8 43.5 + - - +
459A GLN* 3.0 25.4 - - - +
461A CYS* 1.3 71.0 - - + +
463A LEU* 1.3 82.0 + - - +
465A GLU* 4.3 15.7 + - - +
466A LYS 5.3 0.2 + - - -
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Residues in contact with LEU 463 (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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108A ASP* 5.3 2.8 - - - +
109A ASN* 3.0 47.2 - - + +
110A PRO* 3.9 17.9 - - + -
422A THR* 3.5 35.2 - - + +
425A GLU* 5.0 12.3 - - + -
426A VAL* 5.4 2.9 - - + -
459A GLN* 2.8 34.2 + - + +
460A LEU* 3.6 7.2 - - - +
462A VAL* 1.3 78.8 - - - +
464A HIS* 1.3 61.6 + - + +
465A GLU 3.5 2.9 + - - -
466A LYS* 3.6 20.4 - - + +
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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
------------------------------------------------------------
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