Contacts of the helix formed by residues 78 - 90 (chain A) in PDB entry 4ZZ7
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 HIS 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 2.8 44.2 + - - +
75A LEU 3.5 3.1 - - - -
76A GLU 3.3 0.2 - - - -
77A GLN* 1.3 83.1 + - + +
79A ALA* 1.3 63.9 + - - +
80A ASP 3.3 2.9 - - - -
81A GLU* 3.2 8.1 + - + +
82A ILE* 3.0 26.5 + - + +
183A TYR* 3.1 35.3 + - + +
187A LEU* 3.5 26.4 - - + +
190A GLU* 4.6 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU 3.1 8.6 + - - +
76A GLU* 3.3 20.2 + - - +
77A GLN 3.3 3.6 + - - -
78A HIS* 1.3 77.8 - - - +
80A ASP* 1.3 65.6 + - - +
82A ILE* 3.6 1.0 + - - +
83A CYS* 3.1 30.8 + - - -
98A MET* 4.1 17.3 - - + -
101A LEU* 3.5 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLN 5.2 0.2 + - - -
78A HIS 3.3 0.8 - - - -
79A ALA* 1.3 81.1 - - - +
81A GLU* 1.3 62.9 + - - +
83A CYS* 3.3 7.3 + - - +
84A ARG* 3.0 23.0 + - - +
98A MET* 5.2 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A HIS* 3.2 11.5 + - + +
80A ASP* 1.3 77.9 - - - +
82A ILE* 1.3 58.0 + - - +
84A ARG* 2.1 46.5 + - - +
85A LEU* 2.9 38.3 + - + +
183A TYR* 3.7 34.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 3.7 30.7 - - + +
78A HIS* 3.0 28.7 + - + +
79A ALA 3.8 3.1 - - - +
81A GLU* 1.3 74.1 - - - +
83A CYS* 1.3 58.6 + - - +
85A LEU* 3.2 8.4 + - - +
86A ILE* 2.9 34.6 + - + +
101A LEU* 4.2 20.6 - - + -
152A VAL* 3.9 27.6 - - + -
180A SER* 5.0 2.5 - - - +
183A TYR* 3.6 22.4 - - + -
184A ILE* 3.9 18.8 - - + -
187A LEU* 4.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ALA 3.1 25.3 + - - +
80A ASP* 3.6 6.5 - - - +
82A ILE* 1.3 76.0 - - - +
84A ARG* 1.3 56.4 + - - +
86A ILE* 3.7 3.7 - - - +
87A GLY* 3.0 23.7 + - - -
92A LYS 4.8 0.7 - - - +
94A ALA* 4.7 10.5 - - + +
97A ALA* 3.6 22.7 - - + +
98A MET* 3.4 50.0 - - + -
101A LEU* 4.3 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASP 3.0 12.4 + - - +
81A GLU* 2.1 63.7 + - - +
83A CYS* 1.3 73.0 - - - +
85A LEU* 1.3 87.3 + - - +
86A ILE 3.2 0.2 - - - -
87A GLY* 3.7 2.0 - - - +
88A GLU* 2.9 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 6.1 1.8 - - - +
81A GLU* 2.9 17.0 + - - +
82A ILE* 3.6 8.3 - - - +
84A ARG* 1.3 115.4 - - - +
86A ILE* 1.3 62.2 + - - +
88A GLU* 4.0 9.4 - - - +
89A GLU* 3.8 28.6 + - - +
177A ASP* 5.5 0.2 - - - +
179A SER* 3.9 22.4 - - - +
180A SER* 3.9 15.7 + - - -
183A TYR* 3.5 47.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 2.9 26.4 + - + +
83A CYS* 3.7 5.2 - - - +
84A ARG 3.2 0.2 - - - -
85A LEU* 1.3 75.5 - - - +
87A GLY* 1.3 60.5 + - - +
90A HIS* 3.0 39.3 + - + +
92A LYS* 3.4 34.1 - - + -
97A ALA* 4.1 20.6 - - + +
100A GLU* 4.1 18.4 - - + +
101A LEU* 5.4 0.7 - - + +
151A PRO* 4.1 8.3 - - + -
152A VAL* 3.6 24.9 - - + -
177A ASP* 6.1 0.4 - - - -
180A SER* 3.7 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN* 4.9 3.8 - - - +
26A ALA* 6.1 0.5 - - - +
83A CYS 3.0 15.6 + - - -
84A ARG* 3.4 3.1 + - - -
86A ILE* 1.3 76.2 - - - +
88A GLU* 1.3 61.7 + - - +
91A GLY* 3.2 18.6 - - - -
92A LYS 3.5 26.0 - - - -
313A SER* 3.6 20.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE 3.7 1.0 - - - +
24A ASN* 3.5 39.3 - - + +
25A PRO* 3.7 1.8 - - - +
32A LYS* 4.7 18.1 + - + +
84A ARG* 2.9 44.1 + - + +
85A LEU* 4.2 12.0 - - - +
86A ILE 3.2 0.8 - - - -
87A GLY* 1.3 79.3 - - - +
89A GLU* 1.3 64.4 + - + +
179A SER* 5.8 1.4 - - - -
313A SER* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 4.0 0.3 - - - +
22A VAL* 3.6 17.7 - - + +
23A PHE 3.8 10.0 - - - +
25A PRO* 3.4 17.0 - - - +
32A LYS* 3.6 15.2 - - + +
85A LEU* 3.8 13.0 + - - +
86A ILE 3.4 1.4 + - - -
88A GLU* 1.3 90.4 - - + +
90A HIS* 1.3 60.5 + - - +
176A ARG 3.9 7.6 - - - +
177A ASP* 3.3 18.7 - - + +
178A PRO* 3.3 14.9 - - - +
179A SER* 2.7 52.7 + - - -
180A SER 4.1 0.5 + - - -
324A ILE* 3.7 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO* 3.4 11.9 - - - +
86A ILE* 3.0 20.2 + - + +
89A GLU* 1.3 80.0 - - - +
91A GLY* 1.3 56.8 + - - +
92A LYS* 3.3 38.4 + - + -
148A PHE* 3.4 31.8 - + - -
149A ASN* 3.3 28.1 + - - +
151A PRO* 4.8 1.1 - - + -
177A ASP* 3.4 12.8 - - + +
275A SER* 4.8 9.8 - - - -
276A SER* 5.7 0.9 - - - -
278A GLU* 3.5 25.9 + - - +
322A PRO 4.0 11.5 - - - +
324A ILE* 3.8 14.5 - - + +
----------------------------------------------------------
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