Contacts of the helix formed by residues 501 - 521 (chain A) in PDB entry 3OPY
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 CYS 501 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A TYR* 3.8 15.5 - - - -
375A SER* 2.7 37.0 + - - +
378A GLU* 4.2 20.2 - - + -
379A ARG* 4.9 3.3 - - - +
499A ALA 3.7 1.2 + - - -
500A PRO* 1.3 75.0 - - - +
502A ALA* 1.3 66.3 + - - +
503A PHE* 3.9 6.5 - - - -
504A ASP* 3.2 17.8 + - - -
505A ARG* 3.0 22.9 + - - -
742A ASP* 6.0 0.7 - - - -
746A ASN* 3.4 15.3 - - - +
874A ILE* 5.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A CYS* 1.3 70.6 - - - +
503A PHE* 1.3 62.9 + - - +
505A ARG* 3.4 4.5 + - - +
506A PHE* 3.2 18.0 + - - +
742A ASP* 4.0 4.9 - - - +
745A LEU* 3.7 30.7 - - + -
746A ASN* 2.8 34.3 + - - +
749A SER* 4.3 2.9 + - - -
782A TYR* 4.1 4.0 - - + -
786A ILE* 3.5 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A SER* 3.5 26.5 - - - -
374A TYR* 3.6 30.7 - + + -
501A CYS* 3.3 7.6 - - - -
502A ALA* 1.3 78.1 - - - +
504A ASP* 1.4 55.0 + - - +
506A PHE* 3.1 32.4 + + - +
507A LEU* 2.7 57.7 + - + +
533A ILE* 4.4 7.9 - - + -
536A ASN* 4.8 9.4 - - - -
742A ASP* 4.2 5.0 + - - +
782A TYR* 3.8 12.3 + - - +
874A ILE* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PRO 3.8 3.8 - - - +
224A GLY* 5.3 0.2 - - - -
370A THR 3.8 4.9 - - - +
371A ILE* 3.7 9.7 - - + +
372A GLY* 3.0 28.9 + - - -
373A ALA 4.2 0.3 + - - -
374A TYR* 4.4 4.5 + - - -
375A SER* 2.5 48.9 + - - +
500A PRO* 3.8 11.2 - - + -
501A CYS* 3.2 9.4 + - - +
503A PHE* 1.4 76.5 - - - +
505A ARG* 1.4 59.8 + - - +
507A LEU* 4.2 9.1 - - - +
508A ALA* 2.8 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ALA* 4.5 9.4 - - - +
272A LEU* 3.2 29.2 + - + +
273A SER* 3.2 15.9 - - - +
499A ALA* 3.8 14.1 - - - +
500A PRO* 3.0 32.3 + - + +
501A CYS 3.0 17.6 + - - +
502A ALA* 3.5 11.4 - - - +
504A ASP* 1.4 73.5 - - - +
506A PHE* 1.3 61.9 + - - +
508A ALA* 4.4 0.9 - - - +
509A THR* 3.2 28.6 + - - -
749A SER* 3.8 21.3 + - - -
750A GLY 5.3 0.4 - - - +
753A ASP* 2.7 40.2 + - - -
785A LEU* 5.5 0.2 - - - +
786A ILE* 3.2 39.7 + - + +
787A THR* 5.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ALA 3.2 2.2 + - - +
503A PHE* 3.1 35.0 + + - +
505A ARG* 1.3 79.7 - - - +
507A LEU* 1.4 73.6 + - + +
509A THR* 3.3 1.4 + - - -
510A VAL* 3.0 64.9 + - + +
533A ILE* 4.2 20.0 - - + -
536A ASN* 5.0 10.8 - - - -
538A ILE* 5.2 1.8 - - + -
782A TYR* 3.4 38.4 - + + +
785A LEU* 3.8 19.1 - - + -
786A ILE* 3.5 2.2 - - + +
973A LEU* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A SER* 3.8 20.0 - - - +
370A THR 4.0 20.4 - - - +
371A ILE* 4.0 7.0 - - + +
503A PHE* 2.7 45.3 + - + +
504A ASP* 3.8 9.4 - - - +
506A PHE* 1.4 77.4 - - + +
508A ALA* 1.3 56.6 + - - +
510A VAL* 4.3 1.2 - - - +
511A GLN* 3.0 63.1 + - + +
533A ILE* 3.6 34.8 - - + -
538A ILE* 4.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLY 3.3 28.0 - - - +
227A ALA* 3.8 6.5 - - + -
228A ALA* 3.7 17.5 - - - +
371A ILE* 3.7 27.0 - - + +
504A ASP 2.8 19.3 + - - +
507A LEU* 1.3 71.7 - - - +
509A THR* 1.4 60.3 + - - +
512A GLY* 2.9 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ALA* 3.7 15.8 + - - +
230A ARG* 3.6 20.6 + - - +
231A ALA* 3.3 14.1 - - - +
272A LEU* 5.0 3.5 - - - +
505A ARG 3.2 18.9 + - - -
506A PHE 4.0 0.2 - - - -
508A ALA* 1.4 77.7 - - - +
510A VAL* 1.3 57.7 + - - +
513A VAL* 3.1 29.9 + - - +
785A LEU* 3.7 36.3 - - + +
976A VAL* 3.9 2.7 - - + -
980A LEU* 3.6 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A PHE* 3.0 46.0 + - + +
507A LEU 4.3 1.6 - - - +
509A THR* 1.3 73.0 - - - +
511A GLN* 1.3 63.0 + - - +
513A VAL* 3.4 7.9 + - - +
514A ASP* 3.1 21.1 + - - +
538A ILE* 3.4 34.1 - - + -
785A LEU* 4.3 17.7 - - + -
972A GLN 5.7 1.3 - - - +
973A LEU* 5.2 2.9 - - + -
976A VAL* 4.6 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 3.5 16.1 - - + +
357A VAL 4.6 3.8 + - - +
367A THR* 4.2 4.2 + - - -
369A SER 4.6 2.8 + - - -
370A THR* 6.0 0.4 - - - +
371A ILE* 3.4 26.5 + - + +
507A LEU* 3.0 39.1 + - + +
508A ALA 4.4 1.1 - - - +
510A VAL* 1.3 75.3 - - - +
512A GLY* 1.3 52.0 + - - +
514A ASP* 3.3 4.1 + - - +
515A ALA* 2.8 33.4 + - - +
531A ILE* 3.4 41.1 + - + +
532A SER* 3.5 20.2 - - - +
533A ILE* 3.7 3.2 - - - +
538A ILE* 3.7 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ALA 4.4 1.6 - - - -
231A ALA* 3.9 14.1 - - - -
232A VAL* 3.6 21.8 - - - +
356A LEU* 4.2 5.6 - - - +
508A ALA 2.9 19.8 + - - -
509A THR 3.7 1.6 - - - -
510A VAL 3.2 0.2 - - - -
511A GLN* 1.3 73.3 - - - +
513A VAL* 1.4 62.4 + - - +
515A ALA* 3.4 7.3 + - - +
516A VAL* 3.3 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ALA* 4.3 0.9 - - + -
235A ALA* 4.2 16.7 - - + +
239A TYR* 5.3 0.2 - - + -
509A THR 3.1 21.2 + - - +
510A VAL 3.4 4.9 + - - +
512A GLY* 1.4 73.7 - - - +
514A ASP* 1.4 63.8 + - - +
516A VAL* 3.2 7.3 + - - +
517A ARG* 3.1 55.4 + - + +
976A VAL* 3.7 29.4 - - + -
979A LEU* 4.9 8.5 - - + -
980A LEU* 3.9 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A VAL 3.1 14.0 + - - +
511A GLN 3.7 7.0 - - - +
513A VAL* 1.4 74.7 - - - +
515A ALA* 1.4 53.1 + - - +
517A ARG* 3.0 16.1 + - - +
518A ALA* 2.7 34.9 + - - +
531A ILE* 3.7 15.9 - - + +
538A ILE* 4.0 15.2 - - + +
540A ARG* 2.8 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A VAL* 4.5 2.0 - - + -
309A VAL* 4.2 12.6 - - + -
354A VAL* 3.8 25.8 - - + +
356A LEU* 4.0 19.5 - - + -
511A GLN 2.8 16.7 + - - +
512A GLY 3.4 11.4 - - - +
513A VAL 3.3 0.4 - - - -
514A ASP* 1.4 69.5 - - - +
516A VAL* 1.4 62.5 + - - +
518A ALA* 3.3 3.1 + - - +
519A VAL* 3.1 29.1 + - - +
531A ILE* 3.9 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 4.6 12.6 - - + -
232A VAL* 3.2 50.7 - - + +
235A ALA* 3.8 13.9 - - + +
236A GLY* 3.6 26.2 - - - +
239A TYR* 4.2 3.1 - - + -
309A VAL* 5.8 0.4 - - + -
512A GLY 3.3 4.7 + - - +
513A VAL 3.2 8.6 + - - +
515A ALA* 1.4 74.7 - - - +
517A ARG* 1.4 61.9 + - - +
519A VAL* 3.2 10.8 + - - +
520A LEU* 3.2 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TYR* 3.2 39.0 + - + +
513A VAL* 3.1 35.7 + - - +
514A ASP* 3.0 19.9 + - - +
516A VAL* 1.4 74.1 - - - +
518A ALA* 1.3 53.4 + - - +
520A LEU* 2.9 11.3 + - + +
521A GLU* 2.7 56.1 + - - +
540A ARG* 3.5 8.7 - - - +
972A GLN* 3.9 24.0 + - - +
975A ILE* 4.6 9.1 - - - +
976A VAL* 5.0 7.1 - - - +
979A LEU* 4.0 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL* 3.9 14.6 - - + +
514A ASP 2.7 20.0 + - - +
515A ALA 3.4 6.3 - - - +
517A ARG* 1.3 71.7 - - - +
519A VAL* 1.4 60.5 + - - +
521A GLU* 3.9 1.3 - - - -
522A SER* 3.4 21.3 + - - -
529A PRO* 4.2 7.6 - - + +
531A ILE* 3.8 18.6 - - + -
540A ARG* 3.4 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LYS* 5.1 13.7 + - + +
213A ILE* 3.9 20.6 - - + -
307A ALA* 3.5 31.9 - - + -
308A LEU 5.1 1.8 - - - +
309A VAL* 4.0 19.7 - - + -
352A THR* 3.7 16.0 - - + +
354A VAL* 3.8 15.3 - - + +
515A ALA 3.1 19.6 + - - +
516A VAL* 3.4 9.4 - - - +
517A ARG 3.1 0.2 - - - -
518A ALA* 1.4 73.7 - - - +
520A LEU* 1.3 67.4 + - + +
522A SER* 3.2 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LYS* 4.4 19.9 + - + +
213A ILE* 4.8 4.3 - - + -
239A TYR* 3.7 44.0 - - + +
241A CYS* 3.7 28.7 - - - -
516A VAL* 3.3 22.4 - - + +
517A ARG* 2.9 8.8 + - + +
519A VAL* 1.3 72.7 - - + +
521A GLU* 1.3 58.8 + - + +
522A SER 3.0 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ARG* 2.7 39.0 + - - +
518A ALA 3.9 2.0 - - - +
520A LEU* 1.3 71.6 - - + +
522A SER* 1.4 58.5 + - - +
523A THR* 4.9 1.6 + - - +
526A ILE* 3.9 11.8 - - - +
540A ARG* 2.9 43.4 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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