Contacts of the helix formed by residues 483 - 503 (chain A) in PDB entry 4UIS
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 THR 483 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A ALA 5.3 6.1 - - - +
463A ILE* 3.6 33.7 - - + +
464A ASN* 4.0 9.9 - - + +
465A VAL* 4.0 15.6 - - - +
481A THR* 4.7 1.2 + - - -
482A ASP* 1.3 80.5 - - + +
484A ALA* 1.3 59.0 + - - +
485A LYS 3.0 0.2 - - - -
486A ALA* 2.5 32.6 + - + +
487A LEU* 2.8 31.6 + - - +
522A LEU* 4.6 9.0 - - - +
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Residues in contact with ALA 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A VAL 3.3 9.0 - - - +
481A THR* 3.0 21.9 + - - +
482A ASP 3.1 1.0 - - - -
483A THR* 1.3 82.0 + - - +
485A LYS* 1.3 62.2 + - - +
487A LEU* 4.5 2.2 - - - +
488A ALA* 3.1 27.9 + - - +
515A PRO* 4.5 8.2 - - + +
518A VAL* 4.3 21.0 - - + +
519A THR* 3.9 19.7 - - + +
522A LEU* 6.2 2.7 - - + -
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Residues in contact with LYS 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A VAL* 3.2 23.3 - - + +
481A THR 2.7 29.7 + - - -
482A ASP* 3.0 21.4 + - - +
483A THR 3.0 0.6 - - - -
484A ALA* 1.3 79.5 - - - +
486A ALA* 1.3 55.5 + - - +
488A ALA* 4.5 2.1 - - - +
489A ASP* 2.7 32.6 + - - +
515A PRO* 4.9 13.2 - - + -
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Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA 5.8 1.1 - - - +
371A ARG* 2.5 52.3 + - - +
482A ASP 4.1 0.2 + - - -
483A THR* 2.5 24.3 + - - +
485A LYS* 1.3 72.2 - - - +
487A LEU* 1.3 63.8 + - + +
488A ALA 3.2 1.6 - - - -
489A ASP* 2.8 19.7 + - - +
490A VAL 3.0 1.0 + - - -
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Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA* 4.0 27.8 - - + +
303A VAL* 4.4 11.0 - - + -
304A THR* 3.7 24.2 - - + +
368A VAL 4.6 5.2 - - - +
369A ALA* 4.5 21.3 - - + +
371A ARG* 5.4 2.2 - - - +
463A ILE* 5.7 4.9 - - + -
483A THR* 2.8 37.5 + - - +
484A ALA* 4.6 1.6 - - - +
486A ALA* 1.3 80.5 - - + +
488A ALA* 1.3 57.8 + - - +
490A VAL* 3.1 10.2 - - + +
491A ALA* 2.9 30.9 + - - +
518A VAL* 4.6 14.8 - - + -
522A LEU* 5.9 6.3 - - + -
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Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ALA 3.1 20.9 + - - +
485A LYS* 4.5 3.4 - - - +
487A LEU* 1.3 77.5 - - - +
489A ASP* 1.3 56.6 + - - +
491A ALA* 3.6 5.9 - - - +
492A THR* 2.6 37.6 + - - -
513A ALA* 3.7 23.4 - - - +
514A ASP 4.5 3.1 - - - +
515A PRO* 4.5 9.2 - - + -
518A VAL* 4.4 18.2 - - + +
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Residues in contact with ASP 489 (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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371A ARG* 4.3 3.4 - - - +
408A VAL* 4.4 18.1 - - + +
409A PRO* 5.3 2.1 - - - +
410A ALA* 4.1 20.9 + - + +
485A LYS 2.7 26.6 - - - +
486A ALA* 2.8 8.9 + - - +
488A ALA* 1.3 79.1 - - - +
490A VAL* 1.3 62.3 + - - +
492A THR* 2.8 23.7 + - - -
493A VAL* 2.9 17.7 + - - +
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Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A THR* 3.9 15.9 - - + -
365A LEU* 5.7 2.7 - - + -
368A VAL* 4.1 19.3 - - + -
371A ARG* 3.2 23.1 - - - +
376A LEU* 3.9 26.7 - - + -
441A LEU* 5.5 8.1 - - + -
486A ALA 3.0 4.0 + - - -
487A LEU* 3.1 23.6 - - + +
489A ASP* 1.3 77.3 - - - +
491A ALA* 1.3 62.0 + - - +
493A VAL* 3.1 14.5 - - + +
494A LEU* 3.0 27.5 + - + +
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Residues in contact with ALA 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A THR* 3.3 33.9 - - - +
307A ALA* 4.4 7.2 - - + -
308A ALA* 3.3 21.0 - - - +
311A ALA* 6.2 0.4 - - - -
487A LEU 2.9 19.3 + - - +
488A ALA* 3.6 7.9 - - - +
490A VAL* 1.3 77.7 - - - +
492A THR* 1.3 58.7 + - - +
494A LEU* 3.3 3.7 + - - +
495A GLY* 2.9 24.9 + - - -
513A ALA* 5.6 3.1 - - + -
518A VAL* 6.0 0.4 - - + -
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Residues in contact with THR 492 (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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311A ALA* 5.7 4.7 - - - -
408A VAL* 4.7 11.2 - - + -
488A ALA 2.6 19.0 + - - -
489A ASP* 2.8 13.4 + - - -
491A ALA* 1.3 78.6 - - - +
493A VAL* 1.3 63.5 + - - +
495A GLY* 3.2 1.4 + - - -
496A ARG* 2.9 35.4 + - - +
511A VAL* 3.5 26.0 - - + +
512A GLN* 3.9 10.8 - - + +
513A ALA* 3.7 19.3 + - - +
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Residues in contact with VAL 493 (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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376A LEU* 5.1 12.1 - - + -
401A VAL* 5.7 7.0 - - + +
404A LEU* 4.1 7.4 - - - +
405A GLY* 3.9 22.4 - - - +
408A VAL* 3.5 38.8 - - + -
412A ILE* 5.0 9.2 - - + -
441A LEU* 6.4 1.3 - - + -
489A ASP 2.9 13.7 + - - +
490A VAL* 3.1 30.5 - - + +
492A THR* 1.3 76.7 - - - +
494A LEU* 1.3 57.9 + - + +
496A ARG* 3.8 6.1 - - - +
497A ALA* 2.9 28.4 + - - +
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Residues in contact with LEU 494 (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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278A ALA* 6.0 0.4 - - + -
304A THR* 6.0 2.5 - - - +
305A GLN* 4.7 11.2 - - - +
308A ALA* 4.2 10.5 - - + -
363A VAL* 4.1 16.8 - - + -
365A LEU* 3.6 40.2 - - + -
401A VAL* 6.5 0.2 - - - -
441A LEU* 3.9 17.9 - - + -
490A VAL* 3.0 21.6 + - + +
491A ALA* 3.6 6.5 - - - +
493A VAL* 1.3 80.1 - - + +
495A GLY* 1.3 59.7 + - - +
497A ALA* 2.9 10.1 + - + +
498A LEU* 2.9 55.4 + - + +
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Residues in contact with GLY 495 (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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308A ALA* 4.0 11.9 - - - -
311A ALA* 6.2 1.6 - - - -
312A LEU* 4.3 13.8 - - - +
491A ALA 2.9 15.0 + - - -
492A THR* 3.8 0.9 - - - -
494A LEU* 1.3 77.7 - - - +
496A ARG* 1.3 56.3 + - - +
498A LEU* 2.9 20.5 + - - +
499A TYR* 2.9 26.3 + - - +
511A VAL* 5.1 4.0 - - - -
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Residues in contact with ARG 496 (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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404A LEU* 3.1 44.7 - - + +
408A VAL* 5.1 8.5 - - - +
492A THR* 2.9 25.6 + - - +
493A VAL* 3.9 5.2 - - - +
495A GLY* 1.3 75.8 - - - +
497A ALA* 1.3 57.0 + - - +
499A TYR* 3.1 12.6 + - + +
500A GLU 2.9 24.1 + - - -
509A ASP 2.9 30.9 + - - +
510A THR* 3.5 5.9 - - - +
511A VAL* 2.2 59.0 + - + +
512A GLN* 4.9 0.4 - - - +
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Residues in contact with ALA 497 (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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400A GLN* 5.5 2.2 - - + +
401A VAL* 4.1 32.9 - - + +
404A LEU* 3.5 13.9 - - + +
493A VAL 2.9 15.6 + - - +
494A LEU* 3.1 15.3 - - + +
496A ARG* 1.3 79.8 - - - +
498A LEU* 1.3 58.5 + - + +
500A GLU* 3.4 3.4 + - - +
501A LEU* 2.9 29.7 + - - +
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Residues in contact with LEU 498 (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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276A VAL* 5.0 8.5 - - + -
277A VAL 5.4 0.9 - - - +
278A ALA* 5.5 3.4 - - + -
305A GLN* 5.4 0.2 - - - +
308A ALA* 5.1 0.4 - - + -
312A LEU* 3.7 27.8 - - + -
325A VAL* 4.8 18.2 - - + -
327A PHE* 4.1 16.8 - - + -
363A VAL* 3.8 29.6 - - + -
494A LEU* 2.9 39.1 + - + +
495A GLY* 2.9 8.0 + - - +
497A ALA* 1.3 79.8 - - + +
499A TYR* 1.3 52.8 + - - +
501A LEU* 2.9 8.7 + - + +
502A ALA* 2.3 40.9 + - - +
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Residues in contact with TYR 499 (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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312A LEU* 5.8 6.3 - - + +
315A ALA* 5.4 12.3 - - + -
317A ASP* 5.2 14.8 + - + +
321A LEU* 5.3 8.1 - - + -
404A LEU* 6.0 0.2 - - + -
495A GLY 2.9 11.6 + - - +
496A ARG* 3.1 17.0 + - + +
498A LEU* 1.3 76.5 - - - +
500A GLU* 1.3 60.2 + - + +
502A ALA* 3.4 11.9 - - + +
504A GLY* 2.8 65.4 + - - +
509A ASP* 3.0 61.3 + - + -
511A VAL* 5.6 4.9 - - + -
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Residues in contact with GLU 500 (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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400A GLN* 3.1 53.8 + - + +
403A ASP* 5.3 3.6 - - - +
404A LEU* 3.2 35.6 - - + +
496A ARG 2.9 6.7 + - - -
497A ALA 3.8 3.1 - - - +
499A TYR* 1.3 77.5 - - + +
501A LEU* 1.3 56.3 + - - +
503A GLY* 2.8 26.0 + - - -
504A GLY 3.4 11.8 + - - +
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Residues in contact with LEU 501 (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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276A VAL* 3.7 32.0 - - + +
323A ARG* 3.1 23.8 + - - +
361A SER* 3.6 25.6 - - - +
362A PHE 5.3 2.5 - - - +
363A VAL* 4.9 8.5 - - + -
397A VAL* 5.1 16.8 - - + -
400A GLN* 4.3 21.8 - - - +
497A ALA 2.9 18.1 + - - +
498A LEU* 2.9 8.6 + - + +
500A GLU* 1.3 72.5 - - - +
502A ALA* 1.3 65.0 + - - +
503A GLY 3.0 2.9 + - - -
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Residues in contact with ALA 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A VAL* 6.4 0.2 - - - -
321A LEU* 4.0 24.6 - - + +
322A PRO* 3.3 13.7 - - - +
323A ARG* 3.2 33.4 + - + +
325A VAL* 5.0 13.7 - - + -
498A LEU 2.3 28.6 + - - +
499A TYR* 3.4 15.3 - - + +
501A LEU* 1.3 71.7 - - - +
503A GLY* 1.3 56.3 + - - +
504A GLY 4.1 1.1 - - - +
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Residues in contact with GLY 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 4.8 2.1 - - - +
322A PRO* 4.1 13.6 - - - +
323A ARG* 3.6 14.1 - - - -
500A GLU 2.8 12.5 + - - -
501A LEU 3.0 1.6 - - - -
502A ALA* 1.3 78.8 - - - +
504A GLY* 1.3 62.0 + - - +
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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