Contacts of the helix formed by residues 74 - 79 (chain A) in PDB entry 1Z29
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 PRO 74 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 1.3 93.7 - - + +
75A ILE* 1.3 66.4 + - - +
76A PHE* 3.2 32.1 - - + -
77A MET* 2.9 36.0 + - + +
78A ARG* 3.2 9.2 + - - +
236A PRO 5.0 0.9 - - - +
237A MET* 3.3 32.3 - - + +
242A THR* 4.7 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A THR* 4.4 10.5 - - + -
55A SER* 3.9 19.7 - - - +
56A GLN* 3.3 46.4 - - + +
59A ASP* 4.9 6.7 - - + +
73A ALA 3.8 0.4 + - - -
74A PRO* 1.3 69.9 - - - +
76A PHE* 1.3 75.6 + - + +
78A ARG* 3.3 6.1 + - - +
79A VAL* 2.9 37.6 + - + +
237A MET* 2.8 19.0 + - - +
238A THR* 4.4 11.6 - - + +
240A TYR* 3.7 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO* 3.7 28.9 - - + -
75A ILE* 1.3 82.4 - - + +
77A MET* 1.3 79.5 + - - +
79A VAL 3.9 16.8 - - - +
80A PRO* 4.2 5.7 - - - +
81A PHE* 4.8 8.2 + - + +
89A ILE* 6.3 4.5 - - + -
95A THR* 4.4 4.9 + - - +
106A LYS* 6.1 1.3 - - - +
236A PRO 5.8 0.4 - - - -
237A MET 4.8 1.6 - - - -
240A TYR* 3.5 51.1 - + + +
242A THR* 3.9 11.9 - - + -
243A VAL* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 4.2 13.2 - - + -
74A PRO* 2.9 35.4 + - + +
76A PHE* 1.3 97.8 - - - +
78A ARG* 1.3 64.7 + - - +
79A VAL 3.3 0.6 + - - -
80A PRO* 4.0 4.9 - - - +
89A ILE* 6.3 2.5 - - - -
90A PRO* 4.9 13.9 - - + -
95A THR* 3.7 40.1 - - + +
99A THR* 5.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN* 6.0 0.9 - - - -
59A ASP* 2.7 39.3 + - - +
63A GLN* 3.8 32.1 + - - +
73A ALA* 3.1 38.9 - - + +
74A PRO 3.2 10.9 + - - +
75A ILE* 4.0 7.2 - - - +
77A MET* 1.3 80.7 - - - +
79A VAL* 1.3 61.8 + - + +
80A PRO* 3.5 7.4 - - - +
99A THR* 6.0 0.7 - - - +
104A LEU* 4.5 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 4.4 4.0 - - + -
55A SER* 4.2 25.6 - - - +
59A ASP* 4.7 2.5 - - + -
75A ILE* 2.9 33.7 + - + +
76A PHE* 3.9 9.6 - - - +
78A ARG* 1.3 85.8 - - + +
80A PRO* 1.3 68.0 - - - +
81A PHE* 3.3 3.5 + - - +
104A LEU* 3.6 37.0 - - + +
105A LEU 4.1 3.4 - - - +
106A LYS* 3.9 26.5 - - + +
----------------------------------------------------------
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