Contacts of the helix formed by residues 39 - 50 (chain B) in PDB entry 3EHN
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 TYR 39 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.4 8.1 - - + -
35B GLY 3.6 1.6 + - - -
38B LYS* 1.3 92.2 + - + +
40B GLY* 1.3 68.9 + - - +
41B ALA 3.2 2.6 + - - -
42B ARG* 3.2 6.9 + - - -
43B PHE* 2.8 25.7 + - + +
120B ILE* 3.5 50.9 - - + -
123B ILE* 3.3 28.3 - - + +
124B ALA* 3.2 25.4 - - + +
132B GLU* 3.5 28.5 + - + -
135B ILE* 3.7 32.3 - - + -
200B MET* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLY* 2.8 27.1 + - - -
38B LYS 3.9 0.4 - - - -
39B TYR* 1.3 74.0 - - - +
41B ALA* 1.3 60.3 + - - +
43B PHE* 3.5 2.8 + - - +
44B MET* 3.4 25.1 + - - +
200B MET* 4.3 0.9 - - - -
203B TYR* 3.4 39.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLY 4.7 0.6 + - - -
38B LYS 5.7 0.2 - - - -
39B TYR 3.3 0.2 - - - -
40B GLY* 1.3 69.2 - - - +
42B ARG* 1.3 69.5 + - + +
43B PHE 3.1 2.2 - - - -
44B MET* 3.4 10.7 + - - +
45B ASN* 3.1 25.0 + - - +
203B TYR* 4.6 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU 4.9 3.0 + - - -
38B LYS* 2.7 39.5 + - - +
39B TYR* 3.2 4.2 + - - +
41B ALA* 1.3 79.1 - - + +
43B PHE* 1.3 58.9 + - - +
45B ASN* 3.8 5.3 + - - +
46B MET* 3.0 29.1 + - - +
116B PRO* 3.7 12.7 - - + +
119B GLU* 2.6 59.6 + - - +
120B ILE* 3.6 25.6 - - + +
123B ILE* 4.4 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TYR 2.8 18.6 + - - +
40B GLY* 3.7 3.8 - - - +
42B ARG* 1.3 76.5 - - - +
44B MET* 1.3 65.2 + - - +
46B MET* 3.0 9.7 + - + +
47B GLN* 3.0 48.8 + - + +
120B ILE* 4.0 14.1 - - + +
135B ILE* 5.8 1.1 - - + -
138B ILE* 3.9 30.1 - - + -
139B ALA* 4.6 10.8 - - + -
142B VAL* 4.1 16.8 - - + -
200B MET* 4.3 23.1 - - + -
203B TYR* 3.3 27.8 - - + -
204B ASP* 3.9 21.1 - - + -
214B TRP* 4.0 4.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLY 3.4 11.4 + - - +
41B ALA* 3.4 11.3 + - - +
43B PHE* 1.3 71.4 - - - +
45B ASN* 1.3 64.7 + - - +
46B MET 2.9 5.9 + - - -
47B GLN* 3.1 11.6 + - - +
48B GLN* 3.1 29.2 + - - +
202B GLN 4.7 3.4 - - - +
203B TYR* 3.5 39.9 - - + +
205B LEU* 3.9 26.5 - - + -
267B LYS* 4.8 8.1 - - - +
268B MET* 3.5 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA 3.1 17.3 + - - +
42B ARG* 3.9 4.2 - - - +
44B MET* 1.3 77.5 - - - +
46B MET* 1.3 59.0 + - - +
48B GLN* 3.8 12.6 + - - +
49B ARG* 2.9 50.0 + - - +
112B GLN* 5.9 0.6 - - - +
116B PRO* 3.1 38.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ARG 3.0 16.3 + - - +
43B PHE* 3.0 12.5 + - + +
44B MET 2.9 0.6 - - - -
45B ASN* 1.3 76.0 - - - +
47B GLN* 1.3 65.8 + - - +
48B GLN 3.0 1.6 - - - -
49B ARG* 3.0 11.1 + - - -
50B VAL* 3.5 14.2 + - - +
113B ILE* 3.7 20.1 - - + +
116B PRO* 3.7 16.4 - - + -
117B TRP* 3.3 31.9 - - + -
120B ILE* 3.4 28.0 - - - -
139B ALA* 3.3 28.3 - - - +
142B VAL* 4.0 9.4 - - + -
143B ARG* 3.6 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.0 43.0 + - + +
44B MET* 3.1 12.3 + - - +
46B MET* 1.3 75.3 - - - +
48B GLN* 1.3 61.1 + - - +
50B VAL* 3.6 3.5 + - - +
51B ILE 4.9 0.7 + - - -
53B ILE* 4.9 0.5 - - - +
142B VAL* 4.2 4.2 - - + +
203B TYR 2.6 30.9 + - - -
204B ASP* 3.4 3.6 - - - +
205B LEU* 2.9 28.3 + - + +
206B ILE* 3.3 20.3 + - + +
262B ILE* 3.6 17.5 - - + +
355B TRP* 3.1 39.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B MET* 3.1 20.9 + - - +
45B ASN* 4.0 10.6 - - - +
46B MET 3.0 0.8 - - - -
47B GLN* 1.3 80.0 - - - +
49B ARG* 1.3 63.4 + - + +
50B VAL 3.3 0.2 - - - -
51B ILE 3.4 10.0 - - - +
52B PRO* 3.8 1.0 - - - +
53B ILE* 3.4 54.0 + - + +
54B GLY* 3.5 14.4 - - - -
55B SER 4.2 2.1 + - - -
58B LEU* 5.8 0.9 - - - +
205B LEU* 4.6 4.5 - - + +
262B ILE* 4.3 7.0 - - + -
268B MET* 3.0 38.6 - - - +
270B LEU* 3.9 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASN* 2.9 43.3 + - - +
46B MET* 3.0 4.5 + - - +
48B GLN* 1.3 77.3 - - - +
50B VAL* 1.3 69.3 + - - +
51B ILE* 3.3 0.9 - - - -
52B PRO* 4.2 6.7 - - - +
65B ASP* 4.2 16.8 + - - -
108B ASN 4.0 13.9 - - - +
112B GLN* 3.2 45.6 - - + +
113B ILE* 3.6 36.7 - - + +
146B ALA* 4.9 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B MET 3.5 15.2 + - - +
47B GLN 3.6 0.4 - - - +
48B GLN 3.3 0.4 - - - -
49B ARG* 1.3 80.9 - - - +
51B ILE* 1.3 66.3 + - + +
108B ASN 4.6 0.9 - - - +
113B ILE* 4.3 1.5 - - + +
142B VAL* 3.6 17.5 - - + +
145B ILE* 3.5 31.6 - - + +
146B ALA* 3.9 19.1 - - - +
149B ARG* 3.1 30.0 + - - -
355B TRP* 3.3 46.7 - - + +
----------------------------------------------------------
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