Contacts of the helix formed by residues 469 - 473 (chain B) in PDB entry 1EOB
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 GLY 469 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B TYR* 3.3 16.5 + - - -
345B GLU 4.1 0.2 - - - -
346B VAL 3.7 14.1 - - - -
347B THR 3.8 0.4 - - - -
348B ALA* 3.8 5.2 - - - +
467B ALA 4.8 2.9 + - - -
468B ASP* 1.3 79.3 + - - +
470B TRP* 1.3 61.5 + - - -
471B ALA 3.1 3.1 - - - -
472B GLN* 2.9 33.8 + - - +
473B ARG 3.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 470 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 3.6 28.5 - - + -
70A ILE 4.6 0.4 - - - -
71A TRP* 3.9 28.0 - + + -
92A TRP* 3.7 28.5 - + - -
127A SER* 3.8 28.6 - - - -
128A LEU 4.8 0.8 - - - +
129A ILE* 3.8 24.2 - - + +
140A HIS* 4.1 14.1 + + - -
200A ILE* 3.9 24.5 - - + +
344B SER 3.8 9.0 - - - +
345B GLU* 3.2 10.6 + - + +
347B THR 2.9 18.9 + - - +
348B ALA* 5.0 1.8 - - + -
349B PRO* 4.6 12.1 - - + -
466B ILE* 4.8 5.8 - - + -
469B GLY* 1.3 72.3 - - - -
471B ALA* 1.3 62.7 + - - +
472B GLN 3.0 0.2 - - - -
473B ARG* 3.0 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A HIS* 5.2 2.8 + - - -
200A ILE* 3.7 20.0 - - + +
308B TYR* 4.2 13.0 - - + -
311B ARG* 4.0 7.4 + - - -
341B GLU* 3.3 26.2 - - - +
345B GLU 3.0 15.0 + - - +
469B GLY 3.1 0.2 - - - -
470B TRP* 1.3 76.2 - - - +
472B GLN* 1.3 60.5 + - - +
473B ARG 3.4 0.6 + - - +
528B ARG* 3.1 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 5.0 1.3 - - - +
308B TYR* 3.2 31.9 + - + -
311B ARG* 4.8 2.3 + - - +
386B ASP* 4.8 4.9 - - - +
392B VAL* 5.0 3.5 - - - +
465B LEU 4.6 2.7 - - - +
467B ALA* 3.0 14.7 - - + +
468B ASP* 2.9 37.8 + - - +
469B GLY 2.9 15.8 + - - +
471B ALA* 1.3 79.0 - - - +
473B ARG* 1.3 66.2 + - - +
474B LEU* 3.0 12.5 + - - +
527B LEU* 4.2 25.4 - - + +
528B ARG* 3.0 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.4 1.6 - - - +
69A GLU* 2.9 42.3 + - - -
94A ARG* 3.9 6.9 - - - +
129A ILE* 3.8 17.6 - - + +
131A PHE* 3.8 23.3 - - + -
140A HIS* 4.6 5.9 + - + -
311B ARG* 3.8 14.6 + - - -
464B SER* 2.9 30.0 + - - -
465B LEU 2.9 24.5 + - - -
466B ILE* 3.5 19.6 - - - +
467B ALA 5.8 0.2 - - - +
469B GLY 3.8 3.0 + - - -
470B TRP* 3.0 36.6 + - + +
471B ALA 3.4 1.1 - - - +
472B GLN* 1.3 76.6 - - - +
474B LEU* 1.3 72.8 + - - +
475B ILE* 3.7 15.8 - - - +
----------------------------------------------------------
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