Contacts of the helix formed by residues 120 - 130 (chain E) in PDB entry 3G3B
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 ILE 120 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E LYS 3.6 23.8 - - - +
91E SER* 4.0 23.8 - - - -
92E ILE 5.6 2.0 + - - +
113E TRP* 3.9 22.0 - - + -
114E ASP* 4.1 22.8 - - + +
121E LEU* 1.3 70.4 + - + +
122E TYR* 3.3 2.9 - - - -
123E LEU* 2.8 39.4 + - + +
124E SER* 2.9 12.6 + - - +
147E CYS* 5.7 1.8 - - - -
154E VAL* 3.9 24.5 - - + -
157E VAL* 4.0 26.2 - - + -
162E THR* 4.7 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E ILE* 1.3 83.9 - - + +
122E TYR* 1.3 61.3 + - - +
123E LEU 3.3 0.2 - - - -
124E SER* 4.0 11.7 - - - +
125E ARG* 3.2 36.7 + - - +
157E VAL* 5.1 2.5 - - + +
158E THR 5.0 1.3 - - - -
159E LYS* 4.5 32.5 - - + +
162E THR* 4.2 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 122 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ILE* 4.0 33.4 - - + +
93E PRO 3.7 18.2 - - - -
94E ARG* 4.1 15.9 - - + -
95E GLY* 3.2 25.6 - - - -
96E ALA 3.5 1.9 + - - -
97E PHE* 2.8 43.1 + + - +
98E ASP* 3.1 20.8 + - - -
120E ILE 3.1 1.0 + - - -
121E LEU* 1.3 77.5 - - - +
123E LEU* 1.3 56.1 + - - +
125E ARG* 3.7 27.8 + - - +
126E TRP* 2.8 47.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ILE* 3.8 28.9 - - + +
97E PHE* 4.3 11.7 - - + -
108E LEU* 3.8 26.0 - - + -
113E TRP* 3.9 40.6 - - + +
120E ILE* 2.8 14.8 + - + +
122E TYR* 1.3 78.6 - - + +
124E SER* 1.3 64.0 + - - +
125E ARG 3.2 1.6 - - - -
126E TRP* 3.8 6.5 - - + +
127E ILE* 3.0 41.3 + - + +
145E ALA* 5.3 0.4 - - + -
154E VAL* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 124 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E ILE* 2.9 15.8 + - - -
121E LEU* 4.0 13.2 - - - +
123E LEU* 1.3 77.6 - - - +
125E ARG* 1.3 57.7 + - - +
128E SER* 3.0 24.1 + - - -
154E VAL* 3.0 29.2 + - - +
155E ARG* 3.8 10.4 + - - +
157E VAL* 2.9 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 125 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E ARG* 4.1 26.5 - - - +
121E LEU* 3.2 31.5 + - - +
122E TYR* 3.7 34.5 + - - +
123E LEU 3.2 0.6 - - - -
124E SER* 1.3 77.1 - - - +
126E TRP* 1.3 64.3 + - - +
127E ILE 3.4 0.2 - - - -
128E SER* 3.7 6.7 + - - -
129E GLN* 3.2 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 126 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E PHE* 3.6 48.0 + + + +
98E ASP* 5.0 4.0 + - - -
103E LEU* 4.0 15.7 - - + -
106E ILE* 3.7 32.3 - - + -
108E LEU* 4.4 7.0 - - + -
122E TYR* 2.8 43.7 + + + +
123E LEU* 3.0 8.7 + - + +
125E ARG* 1.3 74.5 - - - +
127E ILE* 1.3 76.2 + - + +
129E GLN* 3.3 10.5 + - - +
130E HIS* 3.0 61.1 + + + +
133E LEU* 3.9 25.6 - - + -
134E VAL* 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E LEU* 4.2 12.1 - - + -
123E LEU* 3.0 27.8 + - + +
124E SER 4.5 0.4 - - - +
126E TRP* 1.3 90.3 - - + +
128E SER* 1.3 65.0 + - - +
130E HIS 3.0 22.7 + - - -
131E PRO* 3.4 5.9 - - - +
134E VAL* 4.1 18.8 - - + -
142E HIS* 3.6 30.2 - - + +
145E ALA* 3.8 29.4 - - + +
154E VAL* 4.5 10.8 - - + -
155E ARG* 3.7 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E SER 3.0 15.7 + - - -
125E ARG* 3.7 11.8 + - - -
127E ILE* 1.3 77.9 - - - +
129E GLN* 1.3 57.9 + - - +
130E HIS 3.6 0.3 + - - -
131E PRO* 3.6 7.1 - - - +
142E HIS* 6.1 1.6 - - - -
155E ARG* 3.7 21.7 + - - +
119H ASP* 3.8 27.4 - - - +
122H ALA* 3.1 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E ARG* 3.2 32.6 + - + +
126E TRP* 3.4 12.7 - - - +
127E ILE 3.1 0.8 - - - -
128E SER* 1.3 80.0 - - - +
130E HIS* 1.3 82.2 + - + +
131E PRO* 3.5 2.8 - - - +
132E TRP* 3.3 19.2 - - - -
119H ASP* 5.1 3.1 - - - +
122H ALA* 3.9 11.3 - - - +
125H ARG* 3.8 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E TRP* 3.0 57.7 + + + +
127E ILE 3.0 8.7 + - - +
129E GLN* 1.3 96.1 - - + +
131E PRO* 1.4 56.3 - - - +
132E TRP* 3.2 25.1 - + - -
133E LEU* 3.1 51.4 + - + +
134E VAL* 4.2 8.1 + - - +
125H ARG* 3.9 19.8 + - - -
----------------------------------------------------------
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