Contacts of the helix formed by residues 51 - 57 (chain V) in PDB entry 4ADV
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 LEU 51 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V LEU* 4.1 24.7 - - + -
26V ILE* 4.1 15.3 - - + +
29V ILE* 3.8 38.8 - - + -
30V VAL* 4.4 6.1 - - + -
33V ILE* 4.9 1.6 - - + -
43V GLU* 3.6 16.6 + - - +
46V PRO 5.3 0.4 + - - -
50V ALA* 1.3 77.1 - - + +
52V THR* 1.3 67.0 + - - +
53V GLU 3.3 2.0 - - - -
54V PRO* 3.3 3.9 - - - +
55V VAL* 3.0 30.4 + - + +
111V PHE* 3.9 24.0 - - + -
112V GLY* 4.9 2.9 - - - +
113V ASN* 4.9 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 52 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43V GLU* 2.4 27.0 + - - +
46V PRO* 3.2 17.9 - - + +
49V ALA* 3.3 21.4 + - - -
51V LEU* 1.3 76.5 - - - +
53V GLU* 1.3 56.8 + - - +
55V VAL* 4.8 1.6 - - - -
56V GLY* 2.7 34.7 + - - -
62V LEU* 3.7 22.7 - - + +
64V VAL* 3.9 16.4 - - + -
75V LEU* 4.8 4.3 - - + -
81V LEU* 3.6 12.8 - - + +
85V LEU* 4.4 4.9 - - + -
111V PHE* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48V LEU 5.0 1.9 - - - +
49V ALA* 3.1 24.9 + - + +
50V ALA* 5.2 1.9 - - - +
52V THR* 1.3 77.1 - - - +
54V PRO* 1.3 64.8 - - + +
56V GLY* 3.7 0.3 - - - -
57V GLU* 3.0 31.2 + - - +
78V HIS* 3.1 36.2 + - + +
81V LEU* 3.8 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 54 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23V GLN* 6.1 0.9 - - - +
26V ILE* 4.1 8.1 - - + -
30V VAL* 3.6 32.9 - - + +
50V ALA 3.3 24.5 - - - +
51V LEU 3.3 8.7 - - - +
53V GLU* 1.3 94.0 - - + +
55V VAL* 1.3 64.2 + - - +
57V GLU* 3.6 24.8 - - - +
58V ARG* 3.7 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30V VAL* 4.3 16.6 - - + -
33V ILE* 4.6 13.7 - - + -
35V PRO* 3.9 26.5 - - + -
41V MET* 4.2 3.6 - - + -
51V LEU* 3.0 24.1 + - + +
52V THR 4.1 1.1 - - - +
54V PRO* 1.3 75.4 - - - +
56V GLY* 1.3 63.8 + - - +
58V ARG* 3.0 19.9 + - - +
59V LEU* 3.6 24.2 - - + +
62V LEU* 4.4 2.2 - - + -
111V PHE* 3.8 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 56 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52V THR 2.7 22.8 + - - -
53V GLU 3.7 0.9 - - - -
55V VAL* 1.3 74.1 - - - +
57V GLU* 1.3 58.8 + - - +
59V LEU* 3.0 16.8 + - - +
62V LEU* 3.8 18.1 - - - +
81V LEU* 3.9 11.9 - - - -
84V LYS* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53V GLU 3.0 15.5 + - - +
54V PRO* 3.6 19.8 - - - +
55V VAL 3.2 0.4 - - - -
56V GLY* 1.3 75.3 - - - +
58V ARG* 1.3 61.4 + - + +
59V LEU 3.4 0.7 + - - +
81V LEU* 5.0 0.2 - - - +
84V LYS* 4.0 11.4 + - - +
----------------------------------------------------------
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