Contacts of the helix formed by residues 490 - 511 (chain A) in PDB entry 4I6J
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 ASN 490 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A VAL* 1.3 72.0 - - - +
491A HIS* 1.3 66.6 + - - +
492A ALA* 3.3 11.8 + - - +
493A GLU* 3.1 28.6 + - + +
494A THR* 3.0 23.3 + - - -
261B SER 3.3 22.1 + - - +
262B GLU* 3.7 19.5 + - - +
263B ASN 5.3 4.0 - - - -
296B TYR* 4.1 10.7 + - - -
317B ARG* 5.7 0.5 + - - -
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Residues in contact with HIS 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 4.9 7.6 - - + -
386A GLY* 4.5 6.3 - - - -
387A ASP* 2.7 38.7 + - - +
430A CYS* 5.4 8.9 - - + +
431A TYR 4.2 8.3 - - - -
432A CYS* 3.7 9.7 + - - +
433A PRO* 3.4 35.6 - - + +
489A VAL* 3.4 7.2 + - - -
490A ASN* 1.3 72.4 + - - +
492A ALA* 1.3 51.0 + - - +
494A THR* 3.2 0.4 + - - -
495A SER* 2.7 60.1 + - - -
317B ARG* 2.8 47.4 + - + +
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Residues in contact with ALA 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A ASN* 3.2 11.5 + - - +
491A HIS* 1.3 79.7 - - - +
493A GLU* 1.3 62.9 + - - +
495A SER* 3.4 6.4 - - - -
496A ARG* 3.0 24.8 + - - +
260B VAL* 3.9 8.5 - - + -
261B SER* 3.7 18.2 - - - +
294B PHE* 3.6 30.7 - - + +
296B TYR* 4.6 7.0 - - + -
317B ARG* 4.5 8.1 - - + +
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Residues in contact with GLU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A ASN* 3.1 26.1 + - + +
492A ALA* 1.3 80.5 - - - +
494A THR* 1.3 61.4 + - - +
496A ARG* 2.9 35.5 + - - +
497A LEU* 3.2 35.5 + - + +
181B ASP* 4.7 0.2 - - - +
207B SER* 3.8 11.1 + - - -
260B VAL* 3.8 15.6 - - + +
262B GLU* 5.1 7.0 - - + +
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Residues in contact with THR 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLY 3.2 3.1 - - - +
387A ASP* 3.1 48.4 + - + +
489A VAL* 3.9 16.6 - - - +
490A ASN 3.0 14.3 + - - -
491A HIS 3.5 6.1 - - - -
493A GLU* 1.3 76.8 - - - +
495A SER* 1.3 56.6 + - - +
497A LEU* 2.9 9.6 + - - +
498A ASN* 2.8 46.1 + - - +
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Residues in contact with SER 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLY 4.0 7.8 + - - -
430A CYS* 5.7 1.2 - - - +
491A HIS* 2.7 52.5 + - - -
492A ALA* 3.4 6.3 - - - -
494A THR* 1.3 73.8 - - - +
496A ARG* 1.3 57.2 + - - -
498A ASN* 3.9 1.9 - - - +
499A ILE* 2.9 35.9 + - - +
294B PHE* 3.6 18.4 - - - -
316B GLY 4.3 9.1 + - - -
317B ARG* 5.2 1.0 - - - +
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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
----------------------------------------------------------
492A ALA 3.0 13.1 + - - +
493A GLU* 2.9 38.5 + - - +
495A SER* 1.3 79.6 - - - +
497A LEU* 1.3 80.0 + - - +
499A ILE* 3.9 2.4 + - - +
500A GLU* 3.4 27.5 + - - +
180B ASP* 5.0 4.2 + - - -
181B ASP* 3.5 23.6 + - - -
206B SER* 4.3 10.0 + - - -
207B SER* 3.3 25.0 + - - +
232B ASN* 5.7 0.4 - - - +
256B ARG* 5.6 1.1 - - - +
258B ASP* 3.9 24.3 + - - +
260B VAL* 3.9 21.3 - - + -
294B PHE* 3.2 39.0 - - + -
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLU* 3.2 33.1 + - + +
494A THR* 2.9 12.2 + - - +
496A ARG* 1.3 95.5 - - - +
498A ASN* 1.3 63.0 + - - +
500A GLU* 3.3 7.9 + - + +
501A ARG* 3.1 63.5 + - + +
146B SER* 5.1 1.1 - - - +
148B ALA 4.6 3.6 - - - +
150B PRO* 5.5 13.2 - - + -
181B ASP* 3.8 25.6 - - - +
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Residues in contact with ASN 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ARG 2.9 24.5 + - - +
386A GLY 2.9 31.0 + - - +
387A ASP 3.3 9.0 + - - +
389A TRP* 3.5 24.2 - - + +
494A THR* 2.8 29.0 + - - +
495A SER* 4.0 2.7 - - - +
497A LEU* 1.3 69.7 - - - +
499A ILE* 1.3 66.2 + - - +
501A ARG* 3.1 26.5 + - - +
502A MET* 3.0 28.3 + - - +
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Residues in contact with ILE 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PHE* 4.0 34.9 - - + +
428A PHE* 4.4 2.2 - - - -
495A SER* 2.9 19.7 + - - +
496A ARG* 4.0 6.3 - - - +
498A ASN* 1.3 76.4 - - - +
500A GLU* 1.3 69.0 + - + +
502A MET* 3.5 4.5 + - + +
503A LYS* 2.8 27.2 + - + +
517A LEU* 5.0 4.0 - - + -
256B ARG* 5.5 0.7 - - - +
292B TYR* 4.2 27.6 - - + -
294B PHE* 4.6 4.3 - - + -
314B TYR* 3.6 39.0 - - + +
316B GLY* 5.9 0.2 - - - -
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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
----------------------------------------------------------
496A ARG* 3.4 17.5 + - - +
497A LEU* 3.3 13.6 + - + +
498A ASN 3.2 0.4 - - - -
499A ILE* 1.3 84.5 - - + +
501A ARG* 1.3 58.8 + - + +
503A LYS* 3.0 19.2 - - - +
504A GLN* 2.9 56.2 + - - +
180B ASP* 5.0 14.3 - - - +
256B ARG* 3.5 22.9 + - - +
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Residues in contact with ARG 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PRO* 5.7 1.8 - - + -
389A TRP* 3.8 36.1 - - + +
497A LEU* 3.1 41.9 + - + +
498A ASN* 3.1 30.5 + - - +
500A GLU* 1.3 76.3 - - + +
502A MET* 1.3 67.0 + - - +
504A GLN* 3.2 11.1 + - - +
505A ILE* 2.9 29.9 + - + +
145B ILE* 6.5 0.9 - - + -
146B SER 3.1 17.0 + - - +
147B THR* 2.9 26.5 + - - +
148B ALA* 3.0 32.0 + - - +
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Residues in contact with MET 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ILE* 4.2 17.3 - - + -
338A TRP* 5.2 0.4 - - - -
385A ARG* 4.4 17.0 - - + -
389A TRP* 3.7 24.9 - - + -
419A SER 4.5 1.8 - - - +
420A CYS* 3.9 21.5 - - + +
427A PHE* 3.5 33.7 - - + +
498A ASN 3.0 16.9 + - - +
499A ILE* 3.7 6.5 - - + +
501A ARG* 1.3 73.3 - - - +
503A LYS* 1.3 66.0 + - - +
505A ILE* 2.8 17.6 + - + +
506A TYR* 2.9 49.5 + - + +
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Residues in contact with LYS 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PHE* 4.0 20.1 - - + -
499A ILE* 2.8 20.6 + - + +
500A GLU* 3.0 29.4 + - - +
502A MET* 1.3 74.9 - - - +
504A GLN* 1.3 61.5 + - - +
506A TYR* 3.4 2.1 + - - +
507A GLN* 2.9 59.3 + - + +
515A LEU* 5.1 8.2 + - - +
516A CYS 5.5 1.5 - - - +
517A LEU* 4.7 13.6 - - + +
520A SER* 4.9 4.5 - - - +
256B ARG* 3.6 17.5 - - - +
290B VAL* 5.8 1.2 - - - +
292B TYR* 2.9 29.4 + - - +
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Residues in contact with GLN 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GLU* 2.9 41.6 + - - +
501A ARG* 3.6 11.4 - - - +
503A LYS* 1.3 75.5 - - + +
505A ILE* 1.3 65.2 + - + +
507A GLN* 3.1 12.8 + - - +
508A GLN* 3.1 26.5 + - - +
116B LYS* 5.4 4.9 - - - +
145B ILE* 4.0 34.3 - - - +
180B ASP* 5.9 0.8 + - - -
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Residues in contact with ILE 505 (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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334A ILE* 3.7 28.7 - - + -
335A GLN 4.7 4.7 - - - +
336A ILE* 3.7 24.9 - - + -
337A PRO* 3.4 33.2 - - + -
389A TRP* 4.8 4.9 - - + -
501A ARG* 2.9 17.6 + - + +
502A MET* 2.8 16.9 + - + +
504A GLN* 1.3 76.3 - - + +
506A TYR* 1.3 73.3 + - + +
508A GLN* 3.6 20.7 + - - +
509A LEU* 3.3 19.9 + - + +
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Residues in contact with TYR 506 (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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334A ILE* 3.6 23.9 - - + +
420A CYS* 2.9 28.9 + - + +
421A SER 5.1 0.7 - - - -
422A ALA 5.1 0.9 + - - -
424A PHE* 5.2 5.5 + - - -
425A GLN 3.9 27.7 + - - -
427A PHE* 3.8 24.9 - + + -
502A MET* 2.9 45.1 + - + +
503A LYS 4.1 1.8 - - - +
505A ILE* 1.3 79.6 - - + +
507A GLN* 1.3 59.5 + - - +
509A LEU* 3.2 6.3 + - + +
510A SER* 2.9 25.5 + - - -
520A SER* 3.3 18.5 - - - +
521A VAL* 3.9 10.8 - - + -
522A PRO* 3.7 30.5 - - + -
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Residues in contact with GLN 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A LYS* 2.9 51.7 + - - +
504A GLN* 3.1 13.8 + - - +
506A TYR* 1.3 72.5 - - - +
508A GLN* 1.3 57.1 + - - +
509A LEU 3.0 4.5 - - - -
510A SER* 5.0 1.1 - - - -
511A ARG* 2.8 31.0 + - - -
512A TYR* 3.6 27.8 + - + +
514A GLY 3.9 15.7 - - - +
515A LEU 5.9 0.5 - - - -
516A CYS 5.2 0.5 - - - +
520A SER* 4.1 16.4 + - - -
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Residues in contact with GLN 508 (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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335A GLN 6.0 0.4 + - - -
504A GLN 3.1 12.0 + - - +
505A ILE* 3.8 25.7 - - - +
507A GLN* 1.3 75.6 - - - +
509A LEU* 1.3 62.6 + - + +
511A ARG* 4.0 17.0 + - - +
80B GLU* 5.1 6.6 - - - +
116B LYS* 5.0 17.0 + - - +
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Residues in contact with LEU 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ILE* 4.1 43.1 - - + -
424A PHE* 5.7 4.0 - - + -
505A ILE* 3.3 15.3 + - + +
506A TYR* 3.5 9.6 - - + +
507A GLN 3.0 0.8 - - - -
508A GLN* 1.3 83.6 - - + +
510A SER* 1.3 60.6 + - - +
511A ARG* 3.3 2.9 + - - +
522A PRO* 3.9 23.9 - - + +
526A GLU* 5.2 15.2 - - + +
527A ASP* 4.0 21.5 + - - +
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Residues in contact with SER 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A TYR 2.9 7.2 + - - -
507A GLN 4.2 0.2 - - - -
509A LEU* 1.3 75.7 - - - +
511A ARG* 1.3 67.9 + - - +
512A TYR* 2.8 26.3 + - - +
519A ALA 4.4 2.4 + - - -
520A SER 2.4 31.5 + - - -
521A VAL 4.1 0.2 - - - -
522A PRO* 3.1 20.0 - - - +
527A ASP* 4.5 16.3 - - - +
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Residues in contact with ARG 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A GLN 2.8 12.5 + - - -
508A GLN* 4.0 15.3 + - - +
509A LEU 3.3 2.5 + - - +
510A SER* 1.3 81.3 - - - +
512A TYR* 1.3 62.7 + - - +
513A ARG* 3.0 13.9 + - - +
527A ASP 2.9 33.0 + - - -
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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