Contacts of the helix formed by residues 255 - 260 (chain B) in PDB entry 4AD7
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 TYR 255 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 5.1 0.4 - - + -
42B LYS* 2.5 33.8 + - - -
77B LEU* 3.4 55.2 - - + -
80B ARG* 4.2 5.6 - - + -
81B SER* 4.0 18.6 - - - -
84B GLU* 3.2 19.2 + - - -
251B MET* 3.0 22.7 + - + -
254B VAL* 1.3 96.8 - - + +
256B CYS* 1.3 58.9 + - - +
257B ALA 3.2 2.5 - - - -
258B HIS* 3.1 40.7 + + + +
259B CYS* 3.0 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE 4.4 0.2 - - - -
62B CYS* 2.0 61.9 - - + -
63B PRO* 4.0 6.7 - - + -
251B MET* 3.4 7.9 + - - -
252B LYS* 3.5 38.1 - - - +
254B VAL 3.4 1.0 - - - -
255B TYR* 1.3 76.4 - - - +
257B ALA* 1.3 59.2 + - - +
259B CYS* 3.2 1.8 + - - +
260B LEU* 2.9 34.5 + - - +
416B TRP* 3.9 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B VAL 4.0 11.4 + - - +
255B TYR 3.2 0.6 - - - -
256B CYS* 1.3 76.7 - - - +
258B HIS* 1.3 61.4 - - - +
260B LEU 3.3 0.2 + - - -
261B GLY 3.2 4.9 + - - -
262B VAL* 2.8 48.9 + - - +
265B ALA 4.2 9.2 - - - +
416B TRP* 3.5 45.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 3.3 33.5 - - + +
38B ILE* 3.8 31.5 - - + +
68B CYS* 5.1 1.2 - - - +
69B CYS* 4.8 0.7 - - - -
77B LEU* 5.3 7.0 - - + -
254B VAL* 4.2 9.6 + - + -
255B TYR* 3.2 44.5 - + + +
257B ALA* 1.3 82.3 - - + +
259B CYS* 1.3 60.4 + - - +
260B LEU 3.3 0.5 + - - -
261B GLY* 3.4 9.0 + - - -
262B VAL 4.5 0.2 + - - -
263B PRO* 3.2 44.5 - - + +
265B ALA 5.3 2.5 - - - -
266B ARG* 5.2 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 5.4 1.1 - - + -
62B CYS* 4.0 27.1 - - + -
67B THR* 2.6 36.3 + - - +
68B CYS 3.5 4.1 + - - +
69B CYS* 2.0 51.1 - - + -
74B GLU* 5.1 3.4 - - - -
77B LEU* 4.3 9.4 - - - -
251B MET* 4.4 4.7 - - - -
255B TYR 3.0 15.9 + - - +
256B CYS 3.2 8.2 + - - +
258B HIS* 1.3 77.0 - - - +
260B LEU* 1.3 59.7 + - + +
261B GLY 3.4 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLU* 5.7 0.8 - - - +
59B LEU* 4.8 5.8 - - + -
62B CYS* 5.2 0.9 - - + -
63B PRO* 3.5 48.2 - - + +
64B GLN 5.4 0.2 - - - -
65B GLY* 4.6 17.3 - - - +
66B TYR 4.5 13.5 - - - +
256B CYS* 2.9 17.1 + - + +
257B ALA 3.3 3.1 + - - +
258B HIS 3.2 0.2 - - - -
259B CYS* 1.3 83.9 - - + +
261B GLY* 1.3 59.5 + - - +
262B VAL* 3.6 4.9 - - + +
416B TRP* 3.5 29.6 - - + -
419B MET 3.7 11.7 - - - +
----------------------------------------------------------
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