Contacts of the helix formed by residues 535 - 558 (chain B) in PDB entry 2O2C
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 535 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ASP* 3.9 16.7 + - - +
97B ASN* 3.1 16.4 + - - +
219B LEU* 3.9 5.8 - - - +
222B PHE* 3.8 12.6 - - + -
348B GLU* 6.0 0.4 - - - -
466B GLN* 4.8 2.5 - - - +
533B SER* 3.1 25.1 + - - +
534B LEU* 1.3 75.8 - - - +
536B PRO* 1.4 75.2 - - - +
537B ARG* 3.6 9.4 + - - +
538B ALA* 3.1 20.5 + - - +
539B LEU* 3.1 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 3.7 30.1 - - + -
222B PHE* 3.9 28.3 - - + -
341B ILE* 4.6 0.2 - - + -
345B ASN* 3.3 48.7 - - + +
348B GLU* 4.0 7.9 - - + -
349B LEU* 3.4 17.2 - - - +
535B THR* 1.4 85.0 - - - +
537B ARG* 1.3 61.4 + - - +
539B LEU* 3.3 1.9 + - - +
540B GLY 3.1 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 2.8 47.9 + - + -
92B GLY* 3.6 15.4 + - - -
93B SER* 3.7 25.3 - - - +
97B ASN* 5.6 0.7 - - - +
348B GLU* 2.8 60.7 + - - +
351B THR* 3.6 29.2 + - - +
352B GLY* 3.2 27.6 - - - -
355B VAL* 4.5 1.8 - - - +
535B THR* 3.1 8.6 + - - +
536B PRO* 1.3 79.7 - - - +
538B ALA* 1.3 60.4 + - - +
540B GLY 3.3 0.5 + - - -
541B ALA* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.8 14.3 - - + +
97B ASN* 3.7 8.3 - - - +
531B ILE* 4.0 19.2 - - + +
533B SER 3.3 26.2 - - - +
534B LEU* 4.2 0.4 - - - -
535B THR* 3.1 13.9 + - - +
537B ARG* 1.3 75.1 - - - +
539B LEU* 1.3 66.1 + - - +
541B ALA* 3.3 2.8 + - - +
542B ILE* 3.0 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B MET* 3.9 16.4 - - + -
215B ALA* 4.0 17.7 - - + -
218B ALA* 3.9 19.1 - - + -
219B LEU* 3.9 23.1 - - + -
329B MET* 4.8 0.4 - - + -
349B LEU* 4.0 10.5 - - + -
398B LEU* 3.8 28.0 - - + -
401B LEU* 5.1 0.4 - - + -
534B LEU* 4.1 12.9 - - + +
535B THR 3.1 11.2 + - - +
536B PRO 3.3 7.2 + - - +
538B ALA* 1.3 73.5 - - - +
540B GLY* 1.3 66.5 + - - +
542B ILE* 3.2 8.5 + - + +
543B ILE* 3.0 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B TRP* 3.6 14.2 - - - -
349B LEU* 3.4 28.2 - - - +
353B ALA* 3.5 11.2 - - - +
536B PRO 3.1 10.9 + - - -
537B ARG 3.3 2.0 + - - -
538B ALA 3.3 0.2 - - - -
539B LEU* 1.3 75.5 - - - +
541B ALA* 1.3 56.5 + - - +
544B ALA* 3.1 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 3.6 29.4 - - + -
99B LEU* 4.0 10.8 - - + -
352B GLY 3.5 12.2 - - - +
356B ILE* 3.6 16.9 - - + +
531B ILE* 6.4 0.4 - - + -
537B ARG 3.1 13.1 + - - +
538B ALA* 3.4 10.3 - - - +
540B GLY* 1.3 76.7 - - - +
542B ILE* 1.3 57.6 + - + +
544B ALA* 3.9 0.2 - - - +
545B MET* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.2 20.9 - - + -
398B LEU* 5.0 4.5 - - + -
401B LEU* 4.5 17.7 - - + -
460B ILE* 4.2 22.7 - - + -
529B LEU* 6.1 0.4 - - + -
531B ILE* 4.0 28.7 - - + -
534B LEU* 4.3 11.4 - - + -
538B ALA 3.0 19.2 + - - +
539B LEU* 3.2 10.5 + - + +
541B ALA* 1.3 73.2 - - - +
543B ILE* 1.3 71.2 + - + +
545B MET* 3.3 9.6 + - + +
546B TYR* 3.2 42.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B MET* 3.7 25.6 - - + -
329B MET* 4.1 4.5 - - - -
330B TRP* 3.5 27.1 - - + -
401B LEU* 3.6 31.0 - - + -
404B TYR* 3.6 33.0 - - + +
405B LEU* 4.8 3.1 - - + -
408B LEU* 5.0 0.9 - - + -
539B LEU* 3.0 25.8 + - + +
542B ILE* 1.3 77.6 - - + +
544B ALA* 1.3 57.9 + - - +
546B TYR* 3.1 7.9 + - - +
547B GLU* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ARG* 3.9 12.3 - - - +
330B TRP* 4.4 0.8 - - - -
353B ALA* 3.7 29.2 - - + +
356B ILE* 4.0 10.5 - - + -
357B ASP* 4.1 1.6 - - - +
540B GLY 3.1 19.0 + - - +
541B ALA 3.9 2.9 - - - +
543B ILE* 1.3 76.2 - - - +
545B MET* 1.3 62.8 + - - +
547B GLU* 3.3 12.0 + - - +
548B HIS* 3.0 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.0 13.2 - - + -
356B ILE* 3.8 13.4 - - + +
369B VAL* 3.6 28.0 - - + -
370B PRO* 3.7 15.3 - - + +
373B LEU* 3.8 17.9 - - + -
529B LEU* 3.6 39.0 - - + -
541B ALA 3.0 19.0 + - - +
542B ILE* 3.4 10.5 - - + +
544B ALA* 1.3 76.5 - - - +
546B TYR* 1.3 91.0 + - + +
548B HIS 3.3 1.4 + - - -
549B LYS* 2.9 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU* 4.1 10.1 - - + -
391B ILE* 3.7 13.2 - - + +
405B LEU* 3.7 45.8 - - + -
408B LEU* 4.0 5.4 - - + -
409B ASP* 6.1 0.9 - - - -
458B ASP* 2.7 41.0 + - - +
460B ILE* 3.7 17.0 - - + +
529B LEU* 3.5 8.7 - - - +
542B ILE* 3.2 26.1 + - + -
543B ILE 3.1 8.1 + - - +
545B MET* 1.3 95.7 - - + +
547B GLU* 1.3 64.7 + - - +
549B LYS* 3.3 23.9 + - + +
550B VAL* 3.0 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B HIS* 3.4 8.8 + - - +
152B ARG* 2.7 35.9 + - - -
326B ARG 4.6 0.3 - - - +
327B TYR* 3.6 45.5 + - + -
330B TRP* 2.9 24.7 + - - -
404B TYR* 4.3 3.1 + - - -
408B LEU* 3.9 15.9 - - + -
543B ILE* 2.9 28.0 + - + +
544B ALA* 3.3 7.6 + - - +
546B TYR* 1.3 76.2 - - - +
548B HIS* 1.3 62.0 + - - +
550B VAL* 3.5 4.6 + - - +
551B LEU* 3.1 24.4 + - - +
562B TYR* 4.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 4.0 11.9 - + - -
148B HIS* 4.7 7.4 + - - -
149B ILE* 3.8 19.7 - - + -
152B ARG* 3.7 7.7 + - - -
356B ILE* 4.3 8.3 - - + -
357B ASP* 2.7 34.0 + - - -
360B PHE* 3.5 37.4 - + + -
370B PRO* 3.6 20.2 - - + -
544B ALA 3.0 20.9 + - - +
547B GLU* 1.3 79.1 - - - +
549B LYS* 1.3 61.2 + - - +
551B LEU* 3.3 13.4 + - + +
552B VAL* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B PRO* 3.7 15.6 - - - +
373B LEU* 3.9 29.8 - - + +
374B ALA* 3.5 20.4 - - - +
377B GLY* 5.2 2.5 - - - -
389B HIS* 3.6 35.4 + - - -
409B ASP* 4.3 14.8 + - - +
430B PRO* 6.1 1.4 - - - +
458B ASP* 4.6 3.6 + - - -
545B MET 2.9 17.2 + - - +
546B TYR* 3.3 25.3 + - + +
548B HIS* 1.3 74.8 - - - +
550B VAL* 1.3 64.9 + - + +
552B VAL 3.3 1.7 + - - -
553B GLN* 3.1 51.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TYR* 3.7 13.7 - - - +
408B LEU* 4.0 11.2 - - + +
409B ASP* 4.0 34.1 - - + +
412B SER* 3.5 31.9 - - - +
413B ASN* 3.1 21.4 + - - +
546B TYR* 3.0 19.5 + - + +
547B GLU* 3.6 6.3 - - - +
549B LYS* 1.3 78.6 - - + +
551B LEU* 1.3 62.4 + - - +
553B GLN* 3.5 2.9 + - - +
554B GLY* 3.0 20.8 + - - -
561B SER* 3.8 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 5.3 0.9 - - + -
128B PHE* 3.7 30.2 - - + -
129B VAL* 4.0 21.1 - - + -
132B VAL* 4.2 24.2 - - + -
133B PHE* 5.0 2.7 - - + -
148B HIS* 5.7 3.8 - - + +
360B PHE* 4.1 20.2 - - + -
547B GLU 3.1 13.1 + - - +
548B HIS* 3.4 21.1 - - + +
550B VAL* 1.3 76.8 - - - +
552B VAL* 1.3 61.1 + - + +
554B GLY* 3.4 1.0 + - - -
555B ALA* 3.0 30.5 + - + +
561B SER* 4.6 3.2 + - - -
562B TYR* 3.2 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 4.1 18.6 - - + -
360B PHE* 3.6 28.7 - - + -
371B LEU* 3.7 31.2 - - + +
374B ALA* 3.7 21.5 - - + -
375B LEU* 4.9 0.4 - - + -
548B HIS 3.1 15.8 + - - +
551B LEU* 1.3 79.0 - - + +
553B GLN* 1.3 56.8 + - - +
555B ALA* 3.2 5.6 + - - +
556B ILE* 2.9 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ALA* 3.1 30.8 + - + +
377B GLY* 3.6 23.6 - - - -
378B VAL* 3.8 6.4 - - + +
381B ILE* 4.2 7.0 - - - +
409B ASP* 4.4 10.7 - - - +
413B ASN* 3.9 10.6 + - - +
430B PRO* 4.9 1.9 - - - +
549B LYS* 3.1 44.7 + - - +
550B VAL* 4.9 1.6 - - - -
552B VAL* 1.3 73.7 - - - +
554B GLY* 1.3 63.6 + - - +
556B ILE* 3.3 9.0 + - - +
557B TRP* 3.0 58.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PHE* 6.3 0.2 - - - -
413B ASN* 3.8 5.5 - - - +
550B VAL 3.0 11.8 + - - -
551B LEU 3.8 0.2 - - - -
553B GLN* 1.3 76.2 - - - +
555B ALA* 1.3 56.7 + - - +
557B TRP 3.5 0.5 + - - -
558B GLY 3.0 21.7 + - - -
559B ILE* 3.0 33.1 + - - +
561B SER* 3.3 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ARG* 3.9 12.7 + - - +
125B ILE* 3.5 25.0 - - + +
128B PHE* 3.7 35.4 - - + -
551B LEU* 3.0 17.3 + - + +
552B VAL* 3.2 1.5 + - - +
554B GLY* 1.3 74.0 - - - +
556B ILE* 1.3 65.4 + - - +
558B GLY* 3.3 12.3 + - - +
559B ILE 5.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.3 16.8 - - + +
56B TRP* 4.7 0.7 - - + -
119B LEU* 4.1 24.9 - - + -
120B ALA* 5.2 1.8 - - - -
123B ARG* 2.9 37.6 + - + +
125B ILE* 4.0 15.0 - - + -
374B ALA 5.3 0.9 - - - +
375B LEU* 3.5 32.3 - - + -
378B VAL* 4.0 27.4 - - + -
552B VAL* 2.9 32.0 + - + +
553B GLN* 3.3 5.1 + - - +
555B ALA* 1.3 75.2 - - - +
557B TRP* 1.3 63.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ASP* 4.6 3.3 - - - +
50B LEU* 3.9 16.4 - - + +
123B ARG* 3.7 4.6 + - - -
378B VAL* 4.1 16.0 - - + +
381B ILE* 3.8 24.7 - - + -
382B ASN* 2.9 27.5 + - - -
413B ASN* 3.9 10.3 - - + -
418B THR* 4.1 13.0 - - - +
424B VAL* 4.5 4.6 - - + +
426B THR* 3.6 18.7 + - - +
427B LEU 3.5 8.9 + - - -
428B THR* 3.4 44.4 - - + -
429B GLY* 3.4 20.2 - - - -
553B GLN* 3.0 44.1 + - + +
554B GLY 4.0 2.9 - - - +
556B ILE* 1.3 79.7 - - + +
558B GLY* 1.3 61.7 + - - +
559B ILE* 3.6 17.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ARG* 3.5 14.4 - - - -
418B THR* 3.3 9.6 - - - -
419B ARG* 2.9 30.9 + - - +
554B GLY 3.0 6.2 + - - -
555B ALA* 3.3 6.4 + - - -
556B ILE 3.2 4.0 - - - -
557B TRP* 1.3 78.5 - - - +
559B ILE* 1.3 61.0 + - - +
----------------------------------------------------------
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