Contacts of the helix formed by residues 26 - 35 (chain M) in PDB entry 4N3E
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 GLU 26 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M LYS* 2.8 56.8 + - + +
22M ALA 4.2 2.5 - - - -
25M LEU* 1.3 86.0 - - + +
27M ARG* 1.3 69.3 + - - +
28M HIS* 3.3 12.1 - - - -
29M GLN* 3.2 33.8 + - + +
30M VAL* 2.9 17.1 + - + +
158M PHE* 4.5 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M ALA 3.6 14.1 + - - -
23M LEU* 2.7 45.6 + - - +
24M VAL* 3.2 17.1 + - - +
25M LEU 3.6 0.2 - - - -
26M GLU* 1.3 74.6 - - - +
28M HIS* 1.3 54.4 + - + +
29M GLN 2.7 1.9 + - - -
30M VAL* 2.3 28.3 + - - -
31M LEU* 2.7 35.2 + - + +
57M ILE* 5.4 1.3 - - + -
70M HIS* 6.2 3.1 - - - -
72M PHE* 6.1 1.6 - - + -
84M TYR* 4.0 25.5 + - - -
140M ALA* 4.1 15.8 + - - +
143M PHE* 3.5 35.4 - - + -
144M TYR* 6.3 0.2 - - - +
201M 2AN 2.9 29.1 + - - -
202M 2AN 4.0 16.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 28 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M VAL 5.1 0.8 + - - -
25M LEU 3.8 20.2 + - - -
26M GLU* 4.0 15.1 - - - -
27M ARG* 1.3 79.5 + - + +
29M GLN* 1.3 80.4 + - + +
31M LEU* 4.2 1.3 - - - +
32M VAL* 3.6 13.2 + - - +
42M GLY* 3.4 20.3 - - - -
43M GLU* 3.5 34.5 - - - +
44M ILE* 3.9 28.7 + - + +
55M THR* 4.1 22.9 - - + +
57M ILE* 3.7 35.0 - - + +
72M PHE* 5.8 2.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M GLU* 3.2 37.7 + - + +
27M ARG 2.7 2.8 + - - -
28M HIS* 1.3 96.2 + - + +
30M VAL* 1.3 67.2 + - + +
31M LEU 3.2 0.9 - - - -
32M VAL* 3.3 14.1 + - - +
33M LYS* 3.5 40.5 + - - +
42M GLY 4.6 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M ALA* 3.5 31.9 - - - +
26M GLU* 2.9 18.1 + - + +
27M ARG 2.3 17.4 + - - +
29M GLN* 1.3 68.6 - - + +
31M LEU* 1.3 64.5 + - - +
33M LYS* 3.0 7.0 + - + +
34M ALA* 3.0 21.7 + - - +
143M PHE* 4.0 2.9 - - + -
147M VAL* 3.6 16.6 - - + -
158M PHE* 4.2 10.5 - - + -
203M 2AN 3.4 52.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M ARG* 2.7 30.6 + - + +
28M HIS 4.2 5.2 - - - +
30M VAL* 1.3 76.1 - - - +
32M VAL* 1.3 58.7 + - + +
33M LYS 3.4 0.2 + - - -
34M ALA 3.6 0.2 + - - -
35M GLN* 3.4 27.9 + - - +
39M PHE* 3.8 29.0 - - + -
57M ILE* 3.2 32.3 - - + -
68M MET* 4.8 0.4 - - + -
70M HIS* 6.4 0.2 - - + -
143M PHE* 3.8 32.4 - - + -
201M 2AN 3.4 47.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M HIS 3.6 10.5 - - - +
29M GLN* 3.3 10.2 + - - +
30M VAL 3.2 0.6 - - - -
31M LEU* 1.3 75.4 - - + +
33M LYS* 1.3 62.1 + - + +
35M GLN 4.3 1.6 - - - -
36M PRO* 3.6 23.3 - - + +
39M PHE* 4.0 18.6 - - + +
40M LYS 4.1 17.9 - - - +
41M SER* 3.1 40.2 - - - +
42M GLY 3.3 4.3 - - - +
57M ILE* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 33 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M GLN* 3.5 40.8 + - - +
30M VAL* 3.0 8.6 + - + +
32M VAL* 1.3 81.2 - - + +
34M ALA* 1.3 63.6 + - - +
35M GLN 3.2 2.5 + - - -
36M PRO* 3.6 12.1 - - - +
203M 2AN 2.8 68.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M VAL 3.0 14.4 + - - +
31M LEU 3.6 0.6 + - - +
33M LYS* 1.3 77.1 - - - +
35M GLN* 1.3 60.6 + - + +
36M PRO* 3.6 4.9 - - - +
37M HIS* 4.9 2.3 - - - -
143M PHE* 3.9 19.1 - - + -
146M GLN* 2.9 34.3 + - + +
147M VAL* 4.6 0.2 - - + -
203M 2AN 3.5 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 35 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M LEU 3.4 10.7 + - - +
32M VAL 4.0 3.3 - - - +
34M ALA* 1.3 90.7 - - + +
36M PRO* 1.4 59.5 - - - +
37M HIS* 3.1 26.6 - - + -
38M VAL* 3.1 23.2 + - + +
39M PHE* 3.1 22.9 + - + +
139M LYS* 5.2 2.0 + - - +
142M GLU* 5.1 6.7 + - - -
143M PHE* 4.3 12.7 - - + +
146M GLN* 2.6 29.4 + - - +
201M 2AN 3.1 39.6 - - - -
----------------------------------------------------------
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