Contacts of the helix formed by residues 117 - 138 (chain E) in PDB entry 4GDK
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 SER 117 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E CYS* 3.3 15.9 - - - -
116E PRO* 1.3 85.2 - - - +
118E LYS* 1.3 64.1 + - - +
119E ASP* 3.1 18.0 + - - +
120E ALA* 3.3 32.6 + - - +
121E ILE* 3.7 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E THR 4.7 10.3 - - - +
47E LEU* 4.5 16.9 + - + -
50E ASP* 2.4 39.6 + - - -
53E LYS* 6.1 0.9 - - - +
117E SER* 1.3 71.8 - - - +
119E ASP* 1.3 61.2 + - - +
120E ALA 3.2 0.9 - - - -
121E ILE* 3.5 22.9 + - + +
122E GLU* 3.2 24.7 + - - +
154E TRP* 3.7 8.3 - - + -
158E GLN* 4.1 23.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E SER* 3.1 14.6 + - - +
118E LYS* 1.3 79.2 + - - +
120E ALA* 1.3 58.6 + - - +
122E GLU* 3.4 16.9 + - - +
123E ALA* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E TRP* 4.0 8.1 - - + -
114E HIS 5.3 0.4 - - - +
115E CYS* 4.8 5.2 - - - -
116E PRO* 3.9 27.4 - - + -
117E SER* 3.3 19.6 + - - +
118E LYS 3.2 0.2 - - - -
119E ASP* 1.3 81.1 - - - +
121E ILE* 1.3 60.3 + - - +
123E ALA* 3.6 5.5 + - - +
124E HIS* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E TYR* 4.2 22.9 - - + -
46E THR* 3.3 41.1 - - - +
47E LEU* 4.0 13.2 - - + +
79E TRP* 3.6 19.3 - - + -
115E CYS* 3.5 22.9 - - - -
117E SER 3.8 3.4 - - - +
118E LYS* 3.5 18.8 + - + +
119E ASP 3.2 0.4 - - - -
120E ALA* 1.3 75.2 - - - +
122E GLU* 1.3 59.1 + - - +
124E HIS* 3.2 2.8 + - - +
125E PHE* 2.8 28.2 + - - +
154E TRP* 3.5 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E LYS 3.2 10.3 + - - +
119E ASP* 3.4 17.8 + - - +
121E ILE* 1.3 78.2 - - - +
123E ALA* 1.3 57.4 + - - +
125E PHE* 3.3 1.9 + - - +
126E MET* 2.8 44.1 + - + +
150E HIS 5.0 1.2 - - - +
151E LYS* 2.8 47.0 + - - +
154E TRP* 3.5 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E ASP 3.0 17.9 + - - +
120E ALA* 3.8 7.2 - - - +
122E GLU* 1.3 75.5 - - - +
124E HIS* 1.3 57.7 + - - +
126E MET* 3.3 7.0 + - - +
127E SER* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D SER* 3.5 31.3 + - - -
112D PRO* 4.4 12.6 - - + -
113D ASP* 3.8 7.6 + - - -
44E TYR* 5.0 7.6 + + - -
79E TRP* 4.2 12.2 - + + -
80E HIS* 3.3 51.1 + + + +
113E LEU* 5.4 1.3 - - + -
120E ALA 3.1 18.4 + - - +
121E ILE* 3.6 4.3 - - - +
123E ALA* 1.3 74.8 - - - +
125E PHE* 1.3 68.7 + - - +
127E SER* 3.2 6.0 + - - -
128E CYS* 3.1 42.3 + - - -
188E ARG* 5.7 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E TYR* 3.6 25.1 - + + +
121E ILE 2.8 17.0 + - - +
122E GLU 3.5 3.4 - - - +
124E HIS* 1.3 80.0 + - - +
126E MET* 1.3 69.4 + - - +
128E CYS* 3.3 7.3 + - - +
129E MET* 3.1 47.6 + - - +
153E LEU* 4.2 20.4 - - + -
154E TRP* 3.9 25.6 - + + -
157E LEU* 3.6 23.3 - - + -
165E PHE* 4.1 7.2 - + - -
261E PRO* 3.6 27.8 - - + -
262E ASP* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D GLY 5.0 0.7 - - - +
122E GLU* 2.8 33.3 + - + +
123E ALA* 3.8 6.3 - - - +
125E PHE* 1.3 88.5 - - + +
127E SER* 1.3 61.0 + - - +
129E MET* 3.8 12.9 - - + +
130E LYS* 2.9 43.8 + - + +
142E ILE* 4.6 12.6 - - + -
150E HIS* 3.6 59.2 - - + +
153E LEU* 5.2 1.8 - - + -
154E TRP* 5.3 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D PHE* 4.1 5.6 - - - -
109D ALA* 2.8 34.6 + - - +
110D PRO 4.6 0.6 + - - -
111D SER* 4.5 14.4 - - - -
123E ALA* 2.9 23.5 + - - +
124E HIS* 3.2 9.6 + - - -
126E MET* 1.3 76.9 - - - +
128E CYS* 1.3 59.1 + - - +
130E LYS* 4.3 5.1 - - - -
131E GLU* 3.2 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D SER* 4.1 10.8 - - - -
44E TYR* 5.2 1.8 - - - -
124E HIS* 3.1 40.7 + - - -
125E PHE* 3.6 9.6 - - - +
126E MET 3.2 0.2 - - - -
127E SER* 1.3 77.0 - - - +
129E MET* 1.3 60.5 + - - +
131E GLU* 3.4 4.6 + - - +
132E ALA* 2.9 28.6 + - - +
188E ARG* 4.5 16.6 - - - +
262E ASP* 3.7 30.5 - - + +
264E PHE* 3.4 13.1 - - + -
266E HIS* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E PHE* 3.1 43.2 + - + +
126E MET* 3.4 12.5 + - + +
128E CYS* 1.3 77.2 - - - +
130E LYS* 1.3 57.3 + - - +
132E ALA* 3.1 4.7 + - - +
133E ASP* 2.9 29.6 + - - +
142E ILE* 3.9 13.1 - - + +
153E LEU* 3.9 23.8 - - + -
165E PHE* 4.7 0.7 - - + -
169E ASN* 3.6 4.3 - - - +
172E LEU* 3.5 23.5 - - + +
261E PRO 3.3 7.4 - - - +
262E ASP* 3.8 15.9 - - - -
263E ASN* 3.2 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D SER* 3.3 22.8 + - - +
108D PHE* 3.6 20.0 - - + +
109D ALA 5.7 0.9 - - - +
139D TRP* 3.6 1.6 + - - +
140D GLY* 1.3 81.4 - - - +
126E MET* 2.9 31.8 + - + +
127E SER* 4.5 1.6 - - - +
129E MET* 1.3 76.3 - - - +
131E GLU* 1.3 56.9 - - - +
133E ASP* 3.6 1.4 + - - +
134E ALA* 3.1 26.2 + - - +
139E SER* 4.2 4.5 + - - -
142E ILE* 3.6 28.7 - - + +
143E ASN* 4.1 17.9 + - - -
150E HIS* 5.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D PHE* 3.3 43.0 - - + -
110D PRO* 4.4 4.2 - - - +
111D SER* 4.6 2.8 + - - -
114D GLN* 3.4 30.3 + - - +
119D LEU* 4.8 0.2 - - - -
123D PHE* 4.0 11.4 - - + -
127E SER 3.2 20.7 + - - +
128E CYS* 3.7 4.4 - - - +
129E MET 3.2 0.4 - - - -
130E LYS* 1.3 74.7 - - - +
132E ALA* 1.3 64.3 + - - +
134E ALA* 3.5 4.3 - - - +
135E LEU* 3.4 22.1 + - + +
188E ARG* 3.4 15.4 + - - -
200E GLN* 3.3 22.3 + - - +
264E PHE* 4.2 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E CYS 2.9 14.5 + - - +
129E MET 3.3 8.7 - - - +
131E GLU* 1.3 77.4 - - - +
133E ASP* 1.3 58.7 + - - +
135E LEU* 3.0 7.2 + - - +
136E LYS* 3.0 31.8 + - - +
186E PRO* 3.8 14.5 - - + +
262E ASP 3.9 0.7 - - - +
263E ASN* 3.7 27.8 - - + -
264E PHE* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 133 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E MET 2.9 15.0 + - - +
130E LYS 4.1 0.7 - - - +
131E GLU 3.4 0.2 - - - -
132E ALA* 1.3 77.1 - - - +
134E ALA* 1.3 54.7 + - - +
136E LYS* 3.7 9.8 - - - +
137E HIS* 2.5 60.9 + - - -
139E SER 2.9 14.0 + - - -
141E VAL* 3.2 12.7 + - - +
142E ILE* 2.6 54.1 + - + +
172E LEU* 4.1 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ASN* 5.6 5.5 + - - +
107D SER* 4.6 1.3 - - - +
108D PHE* 4.1 19.5 - - + -
123D PHE* 4.4 9.3 - - + -
130E LYS 3.1 15.5 + - - +
131E GLU 3.5 8.3 - - - +
132E ALA 3.1 0.2 - - - -
133E ASP* 1.3 78.4 - - - +
135E LEU* 1.3 59.6 + - - +
138E LYS* 3.2 23.9 + - - +
139E SER* 3.3 26.0 - - - +
183E ARG* 6.0 0.2 - - - -
184E TYR* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D CYS* 4.6 3.4 - - + +
123D PHE* 3.8 23.8 - - + -
131E GLU 3.4 13.7 + - - +
132E ALA 3.0 7.8 + - - +
134E ALA* 1.3 78.8 - - - +
136E LYS* 1.3 59.0 + - - +
183E ARG* 3.5 8.0 - - - +
184E TYR* 3.0 45.8 + - + +
185E ILE 4.7 3.1 - - - +
186E PRO* 4.0 28.3 - - + -
200E GLN* 3.9 25.1 - - + +
201E LYS 5.9 2.2 - - - +
202E LEU* 3.6 30.1 - - + -
264E PHE* 4.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 136 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E ALA 3.0 25.6 + - - +
133E ASP* 4.2 7.2 - - - +
135E LEU* 1.3 77.9 - - - +
137E HIS* 1.3 79.8 + - + +
138E LYS 3.8 0.4 - - - -
172E LEU* 2.7 23.7 + - - +
173E MET* 3.8 10.9 - - - +
182E PHE* 3.5 34.8 - - + +
183E ARG* 3.2 21.7 + - - +
184E TYR 3.6 7.2 - - - +
186E PRO* 3.6 27.8 - - + -
255E SER* 4.7 1.3 - - - +
263E ASN* 2.7 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 137 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E ASP* 2.5 34.4 + - - +
136E LYS* 1.3 93.7 - - + +
138E LYS* 1.3 73.8 + - - +
139E SER 3.2 0.2 - - - -
140E GLN* 3.1 24.7 + - + +
141E VAL* 3.4 35.5 - - + +
172E LEU 3.4 27.6 - - - -
174E GLU 2.6 27.8 + - - -
175E TYR* 4.3 8.3 - - + -
176E PRO* 4.8 8.5 - - + -
182E PHE* 3.8 8.0 - + - -
183E ARG* 5.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E ALA* 3.2 18.8 + - - +
135E LEU 4.7 0.4 + - - -
136E LYS 3.8 0.6 - - - -
137E HIS* 1.3 78.9 - - - +
139E SER* 1.3 64.3 + - - +
140E GLN* 3.0 25.4 + - + +
183E ARG* 3.4 47.0 - - - +
----------------------------------------------------------
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