Contacts of the helix formed by residues 2534 - 2541 (chain B) in PDB entry 5WBY
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 SER2534 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2530B LYS 3.0 17.1 + - - -
2531B GLN* 4.6 0.4 - - - -
2532B ALA 3.5 1.8 - - - -
2533B THR* 1.3 74.1 - - - +
2535B HIS* 1.3 58.1 + - - +
2536B GLU* 3.3 22.9 + - - +
2537B ASN* 3.5 27.5 + - - +
2538B LEU* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS2535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2284B VAL* 4.3 12.1 - - + -
2287B PHE* 4.1 23.8 - + + -
2288B GLU* 2.8 44.5 + - + +
2291B VAL* 5.4 10.1 - - + +
2533B THR* 3.2 14.6 + - + -
2534B SER* 1.3 72.5 + - - +
2536B GLU* 1.3 57.5 + - + +
2538B LEU* 4.3 7.6 - - + -
2539B CYS* 2.9 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2280B LEU* 3.5 27.2 - - + +
2281B MET* 5.8 4.2 - - - +
2284B VAL* 4.0 15.7 - - + +
2534B SER* 3.2 10.8 + - - +
2535B HIS* 1.3 78.3 - - + +
2537B ASN* 1.3 59.4 + - - +
2539B CYS* 3.4 11.9 - - - -
2540B GLN* 2.8 34.6 + - - +
148D GLN* 5.2 1.4 - - - +
172D SER* 6.0 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2537 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2374B LYS* 3.2 38.9 + - + +
2375B ILE* 3.5 19.1 - - + -
2531B GLN* 2.8 36.5 + - - +
2534B SER* 3.2 17.8 + - - +
2536B GLU* 1.3 80.1 - - - +
2538B LEU* 1.3 63.3 + - - +
2540B GLN* 3.6 13.9 + - - +
2541B CYS* 3.6 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU2538 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2287B PHE* 4.1 12.8 - - + -
2375B ILE* 4.0 8.3 - - + -
2379B LEU 5.5 2.5 - - - +
2380B THR* 4.9 9.6 - - - +
2381B ARG 6.1 0.7 - - - +
2532B ALA 3.9 16.6 - - - +
2533B THR* 3.2 31.2 - - - +
2534B SER 2.9 12.9 + - - +
2535B HIS* 4.0 9.2 - - + +
2537B ASN* 1.3 74.4 - - - +
2539B CYS* 1.3 65.2 + - - +
2541B CYS* 3.1 15.2 + - - +
2545B TRP* 3.7 31.4 - - + -
2547B PRO* 3.3 40.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS2539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2275B TYR* 2.7 37.2 + - - +
2280B LEU* 4.0 7.4 - - - -
2283B LYS* 3.7 26.4 + - - +
2284B VAL* 3.7 17.3 - - - +
2287B PHE* 3.8 27.7 - - + -
2535B HIS 2.9 26.2 + - - +
2536B GLU* 3.4 11.7 - - - -
2538B LEU* 1.3 73.3 - - - +
2540B GLN* 1.3 65.9 + - - +
2541B CYS 3.5 4.5 + - - +
2547B PRO* 5.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN2540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2280B LEU* 3.5 24.5 - - + +
2283B LYS* 4.7 18.3 + - + +
2371B PHE* 4.1 15.8 - - - -
2372B PRO* 4.8 8.6 - - + +
2374B LYS* 3.3 43.6 + - + +
2536B GLU* 2.8 26.0 + - - +
2537B ASN* 3.6 10.0 + - - +
2538B LEU 3.2 0.8 - - - -
2539B CYS* 1.3 76.2 - - - +
2541B CYS* 1.3 65.8 + - - +
2542B TYR 3.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS2541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2275B TYR* 5.4 3.5 - - - -
2371B PHE* 4.5 4.9 - - - -
2372B PRO 5.4 4.5 - - - -
2373B GLU* 5.3 9.6 - - + +
2374B LYS* 5.1 6.3 - - - +
2375B ILE* 4.0 13.9 - - - -
2537B ASN 3.6 12.8 + - - -
2538B LEU* 3.1 21.4 + - - +
2539B CYS 3.8 6.1 - - - +
2540B GLN* 1.3 83.8 - - - +
2542B TYR* 1.3 72.8 + - - +
2543B ILE* 3.5 3.3 + - - +
2545B TRP* 3.7 39.0 - - + -
2547B PRO* 4.1 4.9 - - + +
----------------------------------------------------------
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