Contacts of the helix formed by residues 86 - 92 (chain A) in PDB entry 4K71
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 GLU 86 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR 3.4 1.4 + - - -
85A GLY* 1.3 70.7 - - - -
87A MET* 1.3 55.7 + - - +
88A ALA 3.3 0.4 - - - -
89A ASP* 2.9 56.2 + - - +
90A CYS 3.8 1.4 + - - -
105A HIS* 3.6 36.2 - - + +
149B ASN* 3.5 14.2 - - - +
150B LYS* 3.8 21.4 + - - +
153B THR* 2.8 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR 3.1 26.0 - - - +
31A LEU* 4.3 17.5 - - + -
32A GLN* 5.3 3.6 - - - +
78A ALA* 3.9 6.3 - - + +
84A TYR* 3.3 26.2 - - + +
86A GLU* 1.3 71.9 - - - +
88A ALA* 1.3 60.0 + - - +
89A ASP 3.1 2.0 - - - -
90A CYS* 3.0 25.1 + - - +
91A CYS* 3.3 15.1 + - - -
102A PHE* 3.9 28.6 - - + +
105A HIS* 3.4 47.2 - - + +
106A LYS* 4.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ALA 3.4 14.2 + - - +
79A THR* 3.8 25.7 - - - +
81A ARG* 3.7 29.5 + - + +
84A TYR 4.6 0.4 + - - -
85A GLY 3.2 14.9 + - - +
87A MET* 1.3 76.9 - - - +
89A ASP* 1.3 62.7 + - - +
91A CYS* 3.6 5.2 + - - +
92A ALA* 3.3 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ARG* 2.3 33.7 + - - +
86A GLU* 2.9 43.6 + - + +
88A ALA* 1.3 73.6 - - - +
90A CYS* 1.3 65.7 + - - +
92A ALA* 3.1 20.8 + - - +
93A LYS* 3.5 19.0 - - - +
101A CYS* 4.2 7.6 - - - -
105A HIS* 5.4 0.9 - - + -
146B LYS* 6.1 0.9 - - - +
149B ASN* 3.5 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU 4.3 0.2 - - - -
87A MET* 3.0 18.4 + - - +
89A ASP* 1.3 79.3 - - - +
91A CYS* 1.3 56.3 + - - +
93A LYS* 3.1 21.0 + - - +
98A ARG* 3.4 19.6 - - - +
101A CYS* 2.1 67.1 - - + -
102A PHE* 3.3 26.7 - - + -
105A HIS* 3.5 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A CYS* 2.1 58.4 - - + +
78A ALA* 3.7 24.2 - - - -
79A THR* 3.8 23.4 - - + +
87A MET 3.3 6.3 + - - +
88A ALA* 3.9 7.2 - - - +
89A ASP 3.3 0.6 - - - -
90A CYS* 1.3 77.4 - - - +
92A ALA* 1.3 58.6 + - - +
93A LYS 3.2 6.4 + - - +
98A ARG* 4.6 2.7 + - - +
102A PHE* 4.2 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA 3.3 11.7 + - - +
89A ASP* 3.1 16.6 + - - +
91A CYS* 1.3 75.7 - - - +
93A LYS* 1.3 59.5 + - + +
149B ASN* 6.2 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