Contacts of the helix formed by residues 105 - 120 (chain E) in PDB entry 1GZ0
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 105 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E VAL* 3.5 3.1 - - - +
104E THR* 1.3 83.2 + - - +
106E PRO* 1.3 83.8 - - - +
107E HIS* 2.9 25.4 + - - +
108E ASN* 3.2 25.9 + - - +
109E LEU* 3.1 16.8 + - - +
132E ALA* 3.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E THR 3.4 6.7 - - - +
105E ASP* 1.3 92.1 - - - +
107E HIS* 1.3 60.4 + - - +
109E LEU* 3.3 3.5 + - + +
110E GLY 3.1 17.3 + - - -
132E ALA* 3.4 16.3 - - + -
133E GLN* 3.8 11.4 - - + +
135E ASN* 3.4 36.1 - - - +
137E THR* 4.6 4.7 - - + -
138E ALA* 3.4 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D HIS* 6.4 2.5 - + - -
105E ASP* 2.9 19.3 + - - +
106E PRO* 1.3 78.3 - - - +
108E ASN* 1.3 70.1 + - - +
110E GLY 3.3 2.3 + - - -
111E ALA* 3.0 21.5 + - + +
137E THR* 4.3 20.2 - - + +
141E VAL* 3.5 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E VAL* 3.9 16.3 - - + +
105E ASP* 3.2 31.1 + - - +
107E HIS* 1.3 79.6 + - - +
109E LEU* 1.3 60.3 - - - +
111E ALA* 3.7 5.5 - - - +
112E CYS* 2.8 36.6 + - - +
198E GLU* 5.7 2.2 + - - -
226E ASN* 4.6 7.3 - - - +
227E VAL* 4.9 20.3 + - + +
228E SER* 4.5 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E LEU* 4.3 18.3 - - + +
103E VAL* 4.1 12.5 - - + +
105E ASP 3.1 13.4 + - - +
106E PRO* 3.4 8.1 - - + +
108E ASN* 1.3 77.6 - - - +
110E GLY* 1.3 57.4 - - - +
112E CYS* 3.6 4.7 + - - +
113E LEU* 3.2 34.3 + - + +
124E VAL* 5.6 0.2 - - + -
126E VAL* 4.8 9.0 - - + -
131E SER* 6.3 0.2 - - - -
132E ALA* 3.5 25.6 - - + +
133E GLN 3.5 28.9 - - - +
134E LEU* 4.0 11.9 - - + +
138E ALA* 4.4 4.5 - - + -
151E LEU* 4.5 21.5 - - + -
153E ARG* 4.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E PRO 3.1 12.5 + - - -
107E HIS 3.8 2.5 - - - -
109E LEU* 1.3 77.6 - - - +
111E ALA* 1.3 63.0 + - - +
113E LEU* 3.5 3.5 + - - -
114E ARG* 3.1 17.7 + - - +
138E ALA* 3.4 27.1 - - - -
141E VAL* 3.8 7.0 - - - -
142E ALA* 3.1 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ASN* 6.4 2.0 - - + -
229D VAL* 5.6 1.2 - - + +
107E HIS* 3.0 22.1 + - + +
108E ASN* 3.2 8.0 + - - +
110E GLY* 1.3 76.3 - - - +
112E CYS* 1.3 62.6 + - - +
114E ARG* 3.3 9.9 + - - +
115E SER* 3.2 23.0 + - - -
141E VAL* 3.5 14.2 - - + +
228E SER* 3.3 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E LEU* 4.3 5.9 - - + +
100E LEU* 3.6 31.0 - - + -
103E VAL* 5.4 1.6 - - - -
108E ASN* 2.8 21.9 + - - +
109E LEU 3.8 1.3 - - - +
111E ALA* 1.3 74.7 - - - +
113E LEU* 1.3 59.5 + - - +
115E SER* 3.4 3.8 + - - -
116E ALA* 2.9 29.2 + - - +
124E VAL* 6.5 0.2 - - - -
227E VAL* 4.1 20.6 - - - -
228E SER* 4.2 7.9 - - - +
231E THR* 3.5 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E LEU* 5.5 0.6 - - + +
109E LEU* 3.2 24.1 + - + +
110E GLY* 3.7 7.4 - - - +
111E ALA 3.4 0.2 - - - -
112E CYS* 1.3 73.1 - - - +
114E ARG* 1.3 66.2 + - - +
116E ALA* 3.2 5.7 + - - +
117E ASP 2.9 19.9 + - - -
124E VAL* 3.8 32.8 - - + -
134E LEU* 4.4 27.8 - - + -
138E ALA* 5.5 0.7 - - + +
142E ALA* 4.2 12.6 - - + -
145E ALA* 3.4 13.5 - - + +
146E ALA* 4.4 13.5 - - + -
149E VAL* 4.0 28.6 - - + +
151E LEU* 4.6 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D GLU* 3.0 35.5 + - - +
224D SER* 2.9 35.9 + - - +
225D LEU* 3.3 15.9 + - + -
226D ASN* 3.5 28.4 - - - +
110E GLY 3.1 13.9 + - - +
111E ALA* 3.3 11.9 - - - +
113E LEU* 1.3 78.7 - - - +
115E SER* 1.3 63.5 + - - +
117E ASP* 3.2 4.7 + - - +
118E ALA* 3.1 19.8 + - - +
141E VAL* 3.6 17.2 + - - +
142E ALA 4.0 9.9 - - - +
143E CYS* 4.0 27.6 - - + +
145E ALA* 3.8 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D LEU* 3.7 18.2 - - - +
229D VAL* 3.4 28.2 - - - +
111E ALA 3.2 10.2 + - - -
112E CYS* 3.9 7.4 - - - -
114E ARG* 1.3 75.0 - - - +
116E ALA* 1.3 67.5 + - - +
118E ALA* 3.2 2.4 + - - +
119E ALA* 2.9 24.8 + - - +
228E SER 4.4 2.3 + - - -
231E THR* 5.0 1.1 - - - -
232E GLY* 4.2 21.0 - - - -
235E LEU* 4.0 6.7 - - - -
236E PHE* 4.2 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E LEU* 4.2 8.7 - - + -
112E CYS 2.9 15.8 + - - +
113E LEU* 3.3 11.0 - - - +
115E SER* 1.3 78.5 - - - +
117E ASP* 1.3 60.8 + - - +
119E ALA* 3.2 1.9 + - - +
120E GLY 3.0 18.0 + - - -
121E VAL* 3.1 24.0 + - + +
124E VAL* 3.9 26.5 - - + -
149E VAL* 4.7 3.4 - - + -
235E LEU* 3.7 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ALA 3.8 8.6 - - - +
222D VAL* 5.5 4.1 - - - +
223D SER* 2.5 36.5 + - - -
113E LEU 2.9 12.5 + - - +
114E ARG 3.3 9.2 - - - +
116E ALA* 1.3 76.3 - - - +
118E ALA* 1.3 64.7 + - - +
120E GLY* 2.9 15.5 + - - +
121E VAL 5.0 0.4 - - - +
145E ALA* 3.6 16.6 - - + -
148E SER* 2.6 35.9 + - - -
149E VAL* 3.7 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D PRO 4.0 1.6 - - - +
218D MSE 3.7 21.7 - - - -
219D ALA* 2.8 27.5 + - - +
223D SER* 3.7 16.6 - - - -
224D SER 4.9 1.6 - - - +
225D LEU* 3.5 28.3 - - + -
114E ARG 3.1 5.9 + - - +
115E SER 3.5 7.6 - - - +
117E ASP* 1.3 79.9 + - - +
119E ALA* 1.3 57.3 + - - +
236E PHE* 3.9 11.4 - - + -
239E VAL* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ALA* 3.8 5.2 - - - +
96E PHE* 3.4 17.7 - - + -
115E SER 2.9 16.0 + - - +
116E ALA 3.6 4.7 - - - +
117E ASP 3.1 0.2 - - - -
118E ALA* 1.3 76.7 - - - +
120E GLY* 1.3 61.0 + - - +
121E VAL* 4.6 0.9 - - + -
235E LEU* 3.8 23.8 - - + -
236E PHE* 3.9 10.1 - - + -
239E VAL* 3.7 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ALA* 3.6 17.3 - - - -
96E PHE* 3.6 12.6 - - - +
117E ASP 2.9 12.0 + - - -
118E ALA 3.4 0.6 - - - -
119E ALA* 1.3 79.3 - - - +
121E VAL* 1.3 66.0 + - - +
122E HIS* 3.6 14.6 + - - -
----------------------------------------------------------
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