Contacts of the helix formed by residues 400 - 414 (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 ARG 400 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 5.1 10.7 - - - +
213B VAL* 3.8 23.8 - - + +
214B MET* 3.9 25.4 + - + +
217B GLU* 4.7 4.3 - - + -
397B TYR 4.7 1.2 + - - -
398B LEU 3.1 0.6 - - - -
399B TRP* 1.3 128.2 + - + +
401B LEU* 1.3 63.6 + - - +
402B PRO* 3.4 2.2 - - - -
403B ALA* 3.5 23.3 + - - +
404B TYR* 3.2 20.6 + - - +
435B GLU* 5.6 2.0 + - - -
399C TRP* 4.7 10.6 - - - -
400C ARG* 4.4 12.3 - - - +
435C GLU* 3.2 39.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B MET* 3.9 16.8 - - + +
391B ILE* 4.6 2.0 - - + -
393B PRO* 4.3 5.8 - - + -
398B LEU* 3.0 45.6 + - + +
400B ARG* 1.3 76.4 - - - +
402B PRO* 1.4 67.5 - - + +
404B TYR* 3.1 3.6 + - + +
405B LEU* 2.9 42.4 + - + +
460B ILE* 3.8 28.9 - - + -
542B ILE* 4.5 9.9 - - + -
543B ILE* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ILE* 3.6 33.9 - - + +
393B PRO* 3.9 13.0 - - + -
398B LEU 3.7 5.2 - - - +
399B TRP* 3.6 15.7 - - - +
400B ARG 3.6 0.4 - - - -
401B LEU* 1.4 92.3 - - + +
403B ALA* 1.3 55.7 - - - +
405B LEU* 3.4 2.2 + - + +
406B GLN* 2.9 31.8 + - - +
432B ILE* 4.2 5.1 - - + +
433B PHE* 4.7 1.8 - - - -
434B GLY* 3.4 34.8 - - - +
435B GLU* 4.1 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 3.6 21.4 - - + +
399B TRP 5.4 0.2 + - - -
400B ARG* 3.5 42.5 + - + +
401B LEU 3.3 0.6 - - - -
402B PRO* 1.3 78.4 - - - +
404B TYR* 1.3 62.8 + - - +
406B GLN* 3.2 26.6 - - - +
407B GLN 3.3 5.4 + - - -
435C GLU* 4.1 12.6 - - + +
443C ALA* 5.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 3.7 15.9 - - + +
211B GLY* 3.4 39.7 - - - -
214B MET* 3.9 23.1 - - + -
326B ARG* 3.6 24.6 + - - -
327B TYR* 4.9 0.7 - - - -
329B MET* 3.4 25.8 + - + +
400B ARG 3.2 11.5 + - - +
401B LEU* 3.1 8.6 + - + +
403B ALA* 1.3 79.7 - - - +
405B LEU* 1.3 69.4 + - + +
407B GLN* 3.2 7.6 + - + +
408B LEU* 3.0 36.0 + - + +
543B ILE* 3.6 29.5 - - + +
547B GLU* 4.3 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ILE* 3.8 37.0 - - + -
401B LEU* 2.9 32.2 + - + +
402B PRO 4.0 3.1 - - - +
404B TYR* 1.3 83.6 - - + +
406B GLN* 1.3 59.0 + - - +
408B LEU* 3.8 17.2 - - + +
409B ASP* 2.9 35.2 + - + +
432B ILE* 4.2 5.0 - - + +
543B ILE* 4.8 3.6 - - + -
546B TYR* 3.7 57.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B PRO 2.9 15.1 + - - +
403B ALA* 3.2 17.6 - - - +
405B LEU* 1.3 76.9 - - - +
407B GLN* 1.3 57.1 + - - +
410B MET* 3.0 54.5 + - - +
432B ILE* 2.8 33.3 + - + +
433B PHE* 4.3 6.1 - - - +
433C PHE* 3.9 20.2 - - - +
434C GLY* 4.7 4.0 + - - +
435C GLU* 3.9 14.6 - - - +
443C ALA 4.2 1.0 - - - +
444C PHE* 3.7 31.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLY 3.3 13.5 - - - +
207B GLY* 3.4 7.0 + - - +
210B LEU* 3.3 31.3 - - + +
326B ARG* 3.8 15.0 - - + +
403B ALA 3.3 2.0 + - - -
404B TYR* 3.2 9.6 + - + +
406B GLN* 1.3 77.3 - - - +
408B LEU* 1.3 65.5 + - - +
411B GLU* 2.9 42.7 + - - +
5002B G6Q 2.5 38.0 + - - -
442C HIS 2.8 12.4 + - - -
443C ALA* 3.3 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ARG* 3.7 22.6 - - - +
327B TYR* 3.4 37.9 - - + +
404B TYR* 3.0 28.0 + - + +
405B LEU* 3.8 27.4 - - + +
406B GLN 3.5 0.2 - - - -
407B GLN* 1.3 77.3 - - - +
409B ASP* 1.3 57.6 + - + +
412B SER* 2.7 31.9 + - - +
543B ILE 4.5 1.6 - - - +
546B TYR* 4.0 5.6 - - + +
547B GLU* 3.9 33.7 - - + +
550B VAL* 4.0 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU* 2.9 21.5 + - + +
408B LEU* 1.3 74.7 - - + +
410B MET* 1.3 59.4 + - - +
412B SER* 3.8 0.2 - - - -
413B ASN* 2.8 42.8 + - - +
429B GLY* 4.5 0.5 - - - -
430B PRO* 3.9 20.7 - - - +
432B ILE* 3.6 29.0 - - + +
546B TYR* 6.1 0.5 - - - -
549B LYS* 4.3 15.6 + - - +
550B VAL* 4.0 21.4 - - + +
553B GLN* 4.4 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLN* 3.0 40.4 + - - +
409B ASP* 1.3 74.6 - - - +
411B GLU* 1.3 58.1 + - - +
414B GLY* 3.0 27.0 + - - -
430B PRO 3.5 16.6 - - - +
431B ILE* 3.9 16.4 - - + -
432B ILE* 3.4 25.6 - - + +
433C PHE* 4.2 15.3 - - + -
443C ALA 4.6 0.4 - - - -
444C PHE* 3.7 24.2 - - + +
446C GLN* 4.1 0.2 - - - +
447C LEU* 3.7 45.9 + - + +
448C ILE* 5.4 0.2 - - + -
455C ILE* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ARG* 3.1 24.2 + - - +
407B GLN* 2.9 29.7 + - - +
410B MET* 1.3 76.2 - - - +
412B SER* 1.3 61.6 + - - +
415B LYS* 3.3 19.2 + - - -
563B ASP 3.8 0.9 - - - +
564B GLN* 4.1 8.7 - - + +
567B VAL* 4.2 12.6 - - - +
5002B G6Q 3.1 30.5 - - - +
441C GLN 4.5 0.3 - - - +
442C HIS* 3.3 29.1 - - - +
443C ALA 3.2 12.8 + - - +
446C GLN* 3.5 22.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ARG* 2.7 18.3 + - - +
327B TYR* 2.9 15.9 + - - -
408B LEU 2.7 23.7 + - - -
409B ASP 3.3 0.8 + - - -
410B MET 3.3 0.2 - - - -
411B GLU* 1.3 80.1 - - - +
413B ASN* 1.3 61.9 + - - +
414B GLY 3.6 0.4 - - - -
415B LYS* 2.8 27.0 + - - +
550B VAL* 3.5 18.8 - - - -
561B SER* 3.2 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ASP* 2.8 24.2 + - - +
410B MET 4.1 0.2 - - - -
412B SER* 1.3 76.2 - - - +
414B GLY* 1.3 55.3 + - - +
415B LYS* 2.9 12.7 + - - -
428B THR* 3.3 5.7 + - - -
429B GLY* 3.0 26.2 + - - -
550B VAL* 3.1 37.4 + - - +
553B GLN* 3.9 11.1 + - - +
554B GLY* 3.8 7.3 - - - +
557B TRP* 3.9 14.8 - - + -
559B ILE* 3.7 13.4 - - + +
561B SER* 2.7 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B MET 3.0 20.2 + - - -
411B GLU 4.5 0.4 - - - -
412B SER 3.6 2.0 - - - -
413B ASN* 1.3 72.4 - - - +
415B LYS* 1.3 60.3 + - - +
428B THR* 4.6 0.9 - - - -
446C GLN* 3.1 30.8 + - - +
447C LEU* 3.8 24.7 - - - +
450C GLN 3.5 9.8 - - - +
451C GLY* 3.9 5.8 - - - -
----------------------------------------------------------
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