Contacts of the helix formed by residues 80 - 98 (chain E) in PDB entry 1ZUM
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 ASP 80 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ARG 3.5 2.9 + - - +
79E MET* 1.3 76.7 - - - +
81E ALA* 1.3 60.7 + - - +
82E SER* 3.9 5.6 - - - +
83E HIS* 2.9 25.8 + - + +
84E ARG* 3.2 8.9 + - - +
127G LYS* 5.5 1.9 + - - -
147H ASP* 3.4 32.7 - - - +
148H GLY* 2.8 18.4 + - - -
498H LYS* 2.7 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E MET 3.5 2.4 + - - -
80E ASP* 1.3 71.1 - - - +
82E SER* 1.3 62.9 + - - +
84E ARG* 3.0 36.1 + - - +
85E GLY 3.2 7.8 + - - -
136E ALA* 3.3 31.5 - - - +
137E ASP* 3.8 13.7 - - + -
145H PRO* 4.0 26.1 + - + +
498H LYS* 4.8 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E ASP* 3.9 2.8 - - - +
81E ALA* 1.3 78.6 - - - +
83E HIS* 1.3 59.1 + - - +
85E GLY* 3.2 5.2 + - - +
86E ARG* 3.0 29.1 + - - +
136E ALA* 5.2 0.2 - - - -
137E ASP* 3.5 28.2 - - - +
127G LYS* 5.3 7.1 - - - -
462G GLN* 4.3 4.7 - - - -
145H PRO 5.1 0.4 + - - -
147H ASP* 2.6 34.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E MET* 3.4 40.2 - - + +
80E ASP* 2.9 21.0 + - + +
82E SER* 1.3 78.5 + - - +
84E ARG* 1.3 64.5 + - - +
85E GLY 3.1 1.6 - - - -
86E ARG* 3.1 19.9 + - + +
87E LEU* 3.0 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E TRP* 3.7 29.5 + - + -
79E MET* 4.0 19.3 + - + -
80E ASP 3.2 9.8 + - - +
81E ALA* 3.0 25.3 + - - +
83E HIS* 1.3 75.6 - - - +
85E GLY* 1.3 61.7 + - - +
87E LEU* 3.3 7.0 + - - +
88E LEU* 3.1 27.5 + - - +
136E ALA* 3.2 22.9 + - + -
183E LEU 3.5 19.1 - - - +
184E ALA* 2.9 26.2 + - - -
185E THR* 4.0 7.6 + - - +
186E GLY* 3.5 18.4 - - - +
213E PHE* 5.0 1.0 - - - -
145H PRO* 6.0 0.4 - - - +
500H SER* 3.7 28.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E ALA 3.2 7.3 + - - -
82E SER* 3.2 5.8 + - - -
83E HIS 3.1 0.8 - - - -
84E ARG* 1.3 80.6 - - - +
86E ARG* 1.3 60.4 + - - +
88E LEU* 3.2 1.8 + - - -
89E ASN* 3.0 31.5 + - - -
133E ALA* 3.5 30.9 - - - +
136E ALA* 3.6 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E SER 3.0 22.2 + - - +
83E HIS* 3.1 27.5 + - + +
85E GLY* 1.3 74.4 - - - +
87E LEU* 1.3 58.5 + - + +
89E ASN* 3.3 33.1 + - - +
90E ARG* 2.9 28.5 + - - +
89G ASN* 4.7 4.6 + - - -
93G ASP* 5.3 3.2 + - - -
96G GLU* 5.2 0.8 + - - -
127G LYS* 6.5 0.9 - - - -
130G ARG* 3.5 59.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E TRP* 4.0 12.6 - - + -
79E MET* 3.5 39.3 - - + -
83E HIS* 3.0 28.7 + - + +
84E ARG 3.6 6.3 - - - +
85E GLY 3.2 0.2 - - - -
86E ARG* 1.3 75.8 - - - +
88E LEU* 1.3 59.8 + - - +
90E ARG* 3.2 4.8 + - + +
91E LEU 2.9 23.9 + - - -
211E ALA* 3.4 26.3 - - - +
212E GLY* 4.0 20.0 - - - +
213E PHE* 3.5 31.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E TRP* 6.3 0.2 - - + -
84E ARG 3.1 18.5 + - - +
85E GLY* 3.2 6.9 + - - +
87E LEU* 1.3 75.2 - - - +
89E ASN* 1.3 57.3 + - - +
91E LEU* 3.4 8.2 + - + +
92E ALA* 3.0 27.0 + - - +
129E LEU* 4.2 31.3 - - + +
132E TYR* 4.3 0.9 - - + -
133E ALA* 3.7 28.9 - - + +
180E GLY* 4.1 9.0 - - - +
183E LEU* 4.1 24.5 - - + -
184E ALA* 3.8 35.9 - - + +
213E PHE* 4.2 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E GLY 3.0 21.7 + - - +
86E ARG* 3.7 30.0 - - - +
88E LEU* 1.3 72.8 - - - +
90E ARG* 1.3 61.5 + - - +
92E ALA* 3.4 6.1 + - - +
93E ASP* 3.0 35.1 + - - +
130E ARG* 3.6 23.6 + - - +
133E ALA* 3.5 20.8 - - - +
86G ARG* 5.1 2.5 + - - -
89G ASN* 4.9 17.2 + - - +
130G ARG* 6.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E ARG 2.9 16.8 + - - +
87E LEU* 3.2 10.3 + - + +
89E ASN* 1.3 73.6 - - - +
91E LEU* 1.3 66.8 + - - +
93E ASP* 3.1 23.2 + - - +
94E LEU* 2.9 55.8 + - + +
97E ARG* 5.2 1.4 - - - +
210E GLU* 4.6 10.9 + - - +
211E ALA* 3.8 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E LEU 2.9 12.9 + - - +
88E LEU* 3.5 13.7 - - + +
90E ARG* 1.3 76.7 - - - +
92E ALA* 1.3 63.5 + - - +
94E LEU* 3.1 6.1 + - - +
95E ILE* 2.9 38.4 + - + +
129E LEU* 4.2 21.3 - - + -
179E LEU* 5.0 7.4 - - + -
183E LEU* 5.5 1.6 - - + -
204E VAL* 4.3 6.3 - - + +
207E LEU* 3.7 39.5 - - + +
208E ILE* 3.8 25.4 - - + +
211E ALA* 3.9 6.0 - - - +
213E PHE* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E LEU 3.0 14.2 + - - +
89E ASN 3.6 7.0 - - - +
90E ARG 3.2 0.2 - - - -
91E LEU* 1.3 76.5 - - - +
93E ASP* 1.3 56.8 + - - +
95E ILE* 3.2 1.1 + - - -
96E GLU* 2.9 24.8 + - - +
126E LEU* 3.2 19.8 - - + +
129E LEU* 4.1 19.3 - - + +
130E ARG* 3.6 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E ASN* 3.0 23.0 + - - +
90E ARG* 3.1 26.0 + - - +
92E ALA* 1.3 75.3 - - - +
94E LEU* 1.3 59.9 + - - +
96E GLU* 3.3 4.5 + - - +
97E ARG* 3.0 26.3 + - - +
130E ARG* 3.0 25.5 + - - +
86G ARG* 4.6 4.7 + - - -
93G ASP* 5.4 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E ARG* 2.9 45.2 + - - +
91E LEU* 3.1 6.7 + - - +
93E ASP* 1.3 74.8 - - - +
95E ILE* 1.3 64.0 + - - +
97E ARG* 3.2 37.1 + - + +
98E ASP* 3.1 25.8 + - - -
207E LEU* 3.5 41.1 - - + +
210E GLU* 3.9 17.3 - - + +
211E ALA* 3.6 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E LEU* 2.9 29.0 + - + +
92E ALA 3.7 4.3 - - - +
94E LEU* 1.3 75.1 - - - +
96E GLU* 1.3 58.0 + - - +
98E ASP 3.2 3.3 - - - -
99E ARG* 2.9 26.2 + - - +
102E LEU* 3.9 13.6 - - + +
122E LEU* 3.7 25.4 - - + -
125E VAL* 4.1 14.8 - - + -
126E LEU* 4.0 12.6 - - + -
129E LEU* 3.6 30.7 - - + -
172E LEU* 6.3 1.1 - - + -
204E VAL* 4.3 17.5 - - + -
207E LEU* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ALA 2.9 16.5 + - - +
93E ASP* 3.6 5.8 - - - +
94E LEU 3.2 0.2 - - - -
95E ILE* 1.3 76.2 - - - +
97E ARG* 1.3 66.0 + - - +
99E ARG* 3.2 33.6 + - - +
126E LEU* 3.8 24.3 - - + +
130E ARG* 2.8 34.8 + - - +
86G ARG* 4.7 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E ARG* 5.2 1.4 - - - +
93E ASP 3.0 14.8 + - - +
94E LEU* 3.2 26.0 + - + +
96E GLU* 1.3 77.3 - - - +
98E ASP* 1.3 89.6 + - - +
99E ARG 3.6 1.6 + - - -
100E THR 5.1 0.3 + - - -
203E TYR* 4.5 2.0 + - - -
207E LEU* 3.6 8.3 - - - +
210E GLU* 2.8 42.0 + - - -
16I GLU* 4.4 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E LEU 3.1 9.3 + - - +
95E ILE 3.2 5.4 - - - +
97E ARG* 1.3 120.0 + - - +
99E ARG* 1.3 57.2 + - - +
100E THR 3.4 2.5 - - - -
101E TYR* 3.3 11.0 + - + -
102E LEU* 2.9 32.7 + - + +
203E TYR* 2.9 33.3 + - + -
207E LEU* 3.6 8.6 - - + +
14I GLN* 5.7 0.5 + - - -
3119I EDO 4.3 12.9 + - - -
----------------------------------------------------------
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