Contacts of the helix formed by residues 139 - 144 (chain E) in PDB entry 3N1Q
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 139 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E GLU* 5.6 1.6 - - - -
55E ARG* 3.9 5.6 - - - +
135E HIS* 3.8 17.6 + - - +
136E ALA* 3.4 25.3 + - - -
137E GLN 3.0 5.1 + - - -
138E ASP* 1.3 83.2 - - - +
140E LEU* 1.3 65.3 + - - +
141E HIS* 3.0 26.6 + - - +
142E TYR* 3.0 25.3 + - - +
143E GLU* 4.4 2.1 - - - +
183E HIS* 5.0 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E GLU* 3.3 41.5 + - + +
55E ARG* 4.2 16.7 - - - +
60E SER* 3.9 13.9 - - - +
61E GLY 5.1 0.2 - - - +
62E PRO 4.7 0.9 - - - +
63E ALA* 4.2 6.7 - - + +
138E ASP 3.4 0.6 + - - -
139E SER* 1.3 72.3 + - - +
141E HIS* 1.3 57.8 + - - +
142E TYR 3.0 0.4 - - - -
143E GLU* 3.0 30.3 + - - +
145E ARG* 3.2 55.9 + - + +
146E ALA* 3.7 15.9 - - + +
183E HIS* 5.7 0.6 - - - -
185E SER* 3.4 18.2 - - - +
186E VAL 4.4 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 141 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E GLU* 3.3 16.7 + - + -
128E GLY 3.1 13.4 + - - +
129E TRP* 3.5 8.3 - - - -
130E ASP* 3.0 24.6 + - + -
135E HIS* 3.7 31.0 + + + +
139E SER* 3.0 16.1 - - - +
140E LEU* 1.3 80.0 - - - +
142E TYR* 1.3 57.1 + - - +
143E GLU 3.1 4.5 + - - -
144E GLY 3.7 0.7 + - - -
146E ALA* 3.1 34.9 + - + +
148E ASP* 2.8 20.2 + - - -
183E HIS* 2.9 20.0 - + - -
190E ZN 2.6 33.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 142 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E GLY 4.9 0.4 - - - +
66E ARG* 3.6 50.9 + - + -
67E VAL* 2.9 33.0 + - - +
129E TRP* 4.1 4.7 - - - -
130E ASP* 3.3 38.4 - - + -
133E GLY* 3.1 22.7 + - - -
135E HIS* 2.7 37.0 + - + -
136E ALA 3.0 22.7 - - - -
137E GLN* 5.1 0.2 - - - -
138E ASP* 4.3 7.4 - - - -
139E SER* 3.0 33.7 + - - +
141E HIS* 1.3 77.4 - - - +
143E GLU* 1.3 61.1 + - + +
144E GLY 3.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ALA* 3.2 30.0 - - - +
64E GLU* 3.3 19.4 + - - +
65E GLY 2.8 30.6 + - - +
67E VAL* 4.0 14.6 - - + +
73E ARG* 3.8 11.9 + - - +
77E LEU* 4.0 6.5 - - - +
100E THR* 3.5 15.6 - - - +
129E TRP* 4.2 3.8 - - - -
138E ASP 4.0 2.4 - - - +
139E SER 4.4 3.1 - - - +
140E LEU* 3.0 14.8 + - - +
142E TYR* 1.3 81.7 - - - +
144E GLY* 1.3 66.1 + - - +
145E ARG* 3.1 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E LEU* 4.4 2.5 - - - -
98E LEU 4.4 0.7 - - - -
99E MET* 3.5 20.5 - - - +
100E THR* 3.2 24.0 + - - +
103E CYS* 3.9 4.7 - - - +
128E GLY 5.1 0.4 - - - -
129E TRP* 3.7 29.3 - - - -
140E LEU 3.5 1.6 + - - -
141E HIS 3.7 5.0 + - - -
143E GLU* 1.3 79.0 - - - +
145E ARG* 1.3 57.7 + - - +
146E ALA 3.4 5.1 + - - -
147E LEU* 5.9 0.7 - - - -
----------------------------------------------------------
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