Contacts of the helix formed by residues 525 - 538 (chain B) in PDB entry 4COO
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 525 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 5.5 2.3 + - - -
445B GLN* 5.0 4.7 - - - +
503B LEU* 4.0 7.2 - - - -
507B HIS* 3.6 42.8 - - - +
508B PHE* 3.8 19.3 - - + -
523B VAL* 4.7 4.0 - - + -
524B VAL* 1.3 82.9 - - - +
526B ALA* 1.3 66.3 + - - +
527B ILE* 3.5 17.8 + - - +
528B ASP* 2.9 30.5 + - - +
529B LEU* 3.3 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A VAL* 3.7 42.4 - - + -
206A VAL* 5.7 0.7 - - + -
210A LEU* 4.8 5.8 - - + -
1554A EDO 4.5 0.6 + - - +
503B LEU* 3.8 24.9 - - + +
507B HIS* 4.5 2.5 + - + +
525B THR* 1.3 75.0 - - - +
527B ILE* 1.3 57.7 + - + +
529B LEU* 3.3 4.6 + - - +
530B LEU* 3.0 29.0 + - - +
1542B ACT 4.4 3.5 - - - +
1546B ACT 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL* 4.2 19.1 - - + -
209A ARG* 3.2 68.9 - - + +
210A LEU* 3.9 20.0 - - + +
213A GLU* 5.5 4.9 - - + -
507B HIS* 5.6 2.5 - - + -
525B THR* 3.2 10.3 + - - +
526B ALA* 1.3 74.9 - - + +
528B ASP* 1.3 62.4 + - - +
530B LEU* 3.7 7.1 - - + +
531B ASN* 2.9 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LEU* 4.6 7.1 - - + +
523B VAL 3.8 7.6 - - - +
524B VAL* 3.5 19.2 - - + -
525B THR* 2.9 37.4 + - - +
527B ILE* 1.3 77.6 - - - +
529B LEU* 1.3 62.7 + - - +
531B ASN* 3.4 10.4 + - - +
532B PHE* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B TRP* 4.2 14.6 - - + -
417B LEU* 4.3 8.3 - - + -
496B LEU* 4.1 38.8 - - + +
499B LEU* 4.3 21.1 - - + -
500B SER* 4.3 7.9 - - - -
503B LEU* 4.5 2.9 - - + -
524B VAL* 5.0 0.4 - - - +
525B THR 3.3 9.0 + - - +
526B ALA* 3.7 8.5 - - - +
527B ILE 3.3 0.2 - - - -
528B ASP* 1.3 79.6 - - - +
530B LEU* 1.3 56.1 + - - +
532B PHE* 3.3 5.1 + - + +
533B VAL* 3.0 41.7 + - + +
1542B ACT 3.9 18.4 - - + +
1546B ACT 3.6 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ARG* 5.5 2.5 - - - +
210A LEU* 3.4 38.4 - - + +
213A GLU* 3.8 28.9 - - + +
214A ILE* 3.9 22.4 - - + -
1554A EDO 3.8 4.7 - - - +
526B ALA 3.0 15.2 + - - +
527B ILE* 3.7 5.8 - - + +
529B LEU* 1.3 76.1 - - - +
531B ASN* 1.3 54.2 + - - +
533B VAL* 3.2 1.3 + - + +
534B ALA* 2.7 48.3 + - + +
1542B ACT 3.2 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLU* 3.7 30.6 + - - +
527B ILE* 2.9 37.3 + - - +
528B ASP* 3.7 10.4 + - - +
529B LEU 3.3 0.2 - - - -
530B LEU* 1.3 76.6 - - - +
532B PHE* 1.3 62.7 + - - +
534B ALA* 4.2 3.8 - - - +
535B ALA* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TRP* 4.3 11.0 - + - -
409B TRP* 4.6 1.3 - - + -
412B LEU* 4.1 22.9 - - + -
416B GLU* 3.4 31.0 - - + -
417B LEU* 3.6 30.5 - - + +
496B LEU* 3.8 23.6 - - + -
528B ASP 3.0 13.3 + - - +
529B LEU* 3.4 7.6 - - + +
531B ASN* 1.3 75.4 - - - +
533B VAL* 1.3 76.1 + - + +
535B ALA* 3.7 3.7 - - - +
536B GLN* 3.0 48.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TRP* 4.0 6.1 - - + -
409B TRP* 3.6 51.1 - - + +
529B LEU* 3.0 27.8 + - + +
530B LEU* 3.9 3.4 - - + +
532B PHE* 1.3 85.1 - - + +
534B ALA* 1.3 63.4 + - - +
536B GLN* 3.4 3.5 + - - +
537B GLU* 3.2 42.7 + - - +
1542B ACT 4.1 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLU* 4.5 20.0 - - + +
530B LEU* 2.7 31.1 + - + +
531B ASN* 4.2 4.0 - - - +
533B VAL* 1.3 73.8 - - - +
535B ALA* 1.3 62.6 + - - +
537B GLU* 3.1 13.7 + - - +
538B ARG* 3.0 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B ASN 3.0 22.3 + - - +
532B PHE* 3.7 3.8 - - - +
534B ALA* 1.3 74.7 - - - +
536B GLN* 1.3 64.2 + - - +
538B ARG* 3.1 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TRP* 3.3 37.6 - - + -
412B LEU* 6.0 1.0 - - - +
532B PHE* 3.0 38.2 + - - +
533B VAL 3.6 4.3 - - - +
535B ALA* 1.3 77.6 - - - +
537B GLU* 1.3 59.9 + - - +
538B ARG 3.6 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B TRP* 3.0 31.4 + - + +
533B VAL* 3.3 26.3 - - - +
534B ALA* 3.1 11.2 + - - +
536B GLN* 1.3 77.2 - - - +
538B ARG* 1.3 57.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ALA 3.0 16.5 + - - +
535B ALA* 3.1 15.5 + - - +
536B GLN 4.0 5.0 - - - +
537B GLU* 1.3 80.3 - - - +
----------------------------------------------------------
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