Contacts of the helix formed by residues 51 - 58 (chain D) in PDB entry 4PEI
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 51 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LEU 3.4 0.8 - - - -
50D ARG* 1.3 120.3 + - + +
52D GLU* 1.3 68.6 + - - +
53D ALA* 3.2 20.0 - - + -
54D ASP* 2.9 40.4 + - - +
67D MET* 3.6 16.4 - - - +
71D HIS* 5.2 0.2 - - - -
74D TYR* 4.1 14.9 + + - -
402D SO4 4.9 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D TYR* 1.3 74.5 - - - +
53D ALA* 1.3 63.7 + - - +
54D ASP 3.0 1.0 + - - -
55D LEU* 3.0 31.0 + - + +
56D VAL* 5.7 0.3 - - - +
67D MET* 3.9 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D TYR* 3.1 19.7 + - + -
52D GLU* 1.3 79.4 - - - +
54D ASP* 1.3 61.7 + - - +
55D LEU 3.1 1.1 + - - -
56D VAL* 3.5 22.6 + - - +
57D TYR* 4.8 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LEU* 3.8 15.8 - - + +
50D ARG* 2.9 52.3 + - - +
51D TYR* 2.9 19.7 + - - +
53D ALA* 1.3 74.7 - - - +
55D LEU* 1.3 64.5 + - - +
56D VAL 3.0 3.4 - - - -
57D TYR* 2.9 20.5 + - - +
58D LEU 3.8 2.8 + - - -
93D SER* 3.3 21.7 + - - +
95D ASN* 2.8 24.1 + - - +
96D VAL* 4.0 0.4 - - - +
402D SO4 4.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LEU* 3.5 23.9 - - + +
52D GLU* 3.0 28.8 + - + +
54D ASP* 1.3 78.6 - - - +
56D VAL* 1.3 63.5 + - + +
57D TYR 3.0 1.6 + - - -
58D LEU* 3.0 13.1 + - + +
65D LYS* 3.0 62.3 + - + +
66D GLN* 3.8 13.0 - - - +
67D MET* 3.9 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D GLU 5.7 0.2 - - - +
53D ALA* 3.6 16.6 - - - +
54D ASP 3.0 0.2 + - - -
55D LEU* 1.3 79.0 - - + +
57D TYR* 1.3 66.9 + - + +
58D LEU 3.5 0.2 - - - -
65D LYS* 4.2 8.3 + - - +
148D PRO* 3.6 38.2 - - + +
151D VAL* 3.7 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ALA 4.8 2.0 - - - -
54D ASP* 2.9 14.3 + - - +
56D VAL* 1.3 92.1 - - + +
58D LEU* 1.3 59.6 + - - +
59D LYS 3.7 1.0 + - - -
92D GLU 3.0 13.5 - - - +
93D SER 4.4 0.7 - - - -
94D SER* 3.6 18.2 + - - +
95D ASN* 3.2 60.1 - - + +
146D PRO* 3.2 31.5 + - + +
147D SER 3.6 20.6 - - - -
148D PRO* 3.3 25.0 - - + +
151D VAL* 3.6 18.4 - - - +
154D LEU* 4.5 10.5 - - + -
402D SO4 3.7 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLN* 4.1 20.2 - - + +
49D LEU* 4.3 22.9 - - + -
54D ASP 3.8 0.6 + - - -
55D LEU* 3.0 16.4 + - + +
57D TYR* 1.3 76.7 - - - +
59D LYS* 1.3 58.4 + - - +
60D VAL* 3.1 39.0 + - + -
64D TYR 3.9 13.2 - - - +
65D LYS* 2.9 28.7 + - + +
66D GLN 3.9 16.2 - - - +
91D HIS* 3.7 8.1 - - - -
92D GLU 3.4 30.5 - - - +
151D VAL* 4.1 1.8 - - - +
----------------------------------------------------------
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