Contacts of the helix formed by residues 46 - 58 (chain B) in PDB entry 3ORH
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 46 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL 5.0 1.4 - - - +
42B MET* 3.3 34.4 - - + +
43B GLU 3.3 12.1 - - - +
44B ARG 3.0 0.4 + - - -
45B TRP* 1.4 103.6 - - + +
47B THR* 1.3 61.8 + - - +
48B PRO* 3.4 1.6 - - - -
49B TYR* 2.9 10.8 + - + +
50B MET* 2.9 39.9 + - + +
135B ASP* 4.9 1.0 - - - +
171B LEU* 3.6 19.0 - - + +
214B LEU* 4.5 3.1 - - - -
222B TYR* 2.4 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU 4.7 0.2 + - - -
44B ARG* 2.7 36.7 + - - +
45B TRP 3.2 1.2 - - - -
46B GLU* 1.3 74.4 - - - +
48B PRO* 1.4 70.0 - - + +
50B MET* 3.2 1.8 + - - +
51B HIS* 2.9 55.7 + - + +
73B ILE* 3.7 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TRP 3.4 14.1 - - - +
46B GLU 3.6 2.0 - - - -
47B THR* 1.4 93.2 - - + +
49B TYR* 1.4 59.4 + - - +
51B HIS* 3.4 13.2 + - + +
52B ALA 3.2 16.3 + - - -
212B MET* 3.8 21.1 - - + +
214B LEU* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 2.9 10.4 + - + +
48B PRO* 1.4 77.2 - - - +
50B MET* 1.4 81.8 + - + +
52B ALA* 3.0 13.7 + - - +
53B LEU* 3.1 23.7 + - + +
168B TYR 4.3 0.2 + - - -
169B CYS* 3.2 28.6 - - + +
171B LEU* 3.4 28.5 - - + -
174B TRP* 3.4 7.2 - + - -
212B MET* 3.8 10.3 - - + -
214B LEU* 4.0 17.0 - - + +
228B MET* 3.4 37.7 - - + -
229B ILE 2.7 24.8 + - - -
230B THR* 3.3 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B MET* 3.5 24.9 - - + -
46B GLU* 2.9 34.5 + - + +
47B THR 3.2 6.7 + - - +
49B TYR* 1.4 103.7 - - + +
51B HIS* 1.4 59.2 + - - +
53B LEU* 3.4 22.0 + - + +
54B ALA* 2.9 29.7 + - - +
73B ILE* 3.7 17.3 - - + -
74B ALA* 3.9 13.9 - - - +
133B LEU* 5.9 0.2 - - - -
135B ASP* 3.5 21.5 - - - +
169B CYS* 4.2 3.1 - - - -
4001B SAH 3.4 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 2.9 42.2 + - + +
48B PRO* 3.4 13.3 - - + +
50B MET* 1.4 76.5 - - - +
52B ALA* 1.4 56.9 + - - +
54B ALA* 3.6 1.6 - - - +
55B ALA* 2.9 30.8 + - - +
73B ILE* 4.2 13.5 + - + +
77B LYS* 3.7 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO 3.2 4.4 + - - -
49B TYR* 3.0 11.5 + - - +
51B HIS* 1.4 72.0 - - - +
53B LEU* 1.3 63.4 + - - +
55B ALA* 3.5 6.7 + - - +
56B ALA* 3.2 22.3 + - - +
210B GLU* 5.1 6.0 - - - +
212B MET* 3.7 27.6 - - + -
230B THR* 3.5 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TYR* 3.1 29.7 + - + +
50B MET* 3.7 29.4 - - + +
51B HIS 3.4 0.2 - - - -
52B ALA* 1.3 72.3 - - - +
54B ALA* 1.3 59.7 + - - +
56B ALA 3.1 2.3 + - - -
57B ALA* 2.9 26.0 + - - +
133B LEU* 3.8 24.0 - - + -
167B THR* 3.3 33.1 - - + +
168B TYR 3.8 18.8 - - - +
169B CYS* 3.6 28.5 - - + -
230B THR* 3.9 13.5 - - + -
231B PRO* 4.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B MET 2.9 17.2 + - - +
51B HIS 3.6 0.2 - - - +
53B LEU* 1.3 75.4 - - - +
55B ALA* 1.4 52.4 + - - +
57B ALA 3.4 0.5 + - - -
58B SER* 2.7 39.3 + - - -
74B ALA* 3.4 27.8 - - - +
77B LYS* 3.5 23.3 - - + -
78B VAL* 3.8 9.9 - - + +
133B LEU* 3.7 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B HIS 2.9 17.8 + - - +
52B ALA* 3.7 7.0 - - - +
53B LEU 3.3 0.2 - - - -
54B ALA* 1.4 74.6 - - - +
56B ALA* 1.4 58.2 + - - +
58B SER* 3.6 5.8 + - - -
59B SER* 3.0 31.0 + - - -
77B LYS* 4.8 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ALA 3.2 12.9 + - - +
53B LEU 3.1 8.2 + - - +
55B ALA* 1.4 75.3 - - - +
57B ALA* 1.4 60.5 + - - +
59B SER* 2.8 25.8 + - - -
165B VAL* 3.2 14.2 - - + +
167B THR* 3.9 20.4 - - - +
210B GLU* 5.6 0.7 - - - +
230B THR* 4.4 3.8 - - + -
232B LEU* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU 2.9 18.8 + - - +
54B ALA* 4.1 3.4 - - - +
56B ALA* 1.4 72.5 - - - +
58B SER* 1.3 58.5 + - - +
59B SER 3.4 0.4 + - - -
60B LYS 4.8 1.4 + - - -
61B GLY 5.1 0.3 - - - +
64B VAL* 3.5 19.1 - - + +
78B VAL* 5.0 0.9 - - + -
130B ASP 4.8 0.2 - - - -
131B GLY* 3.3 22.9 - - - -
132B ILE 3.9 12.8 - - - +
133B LEU* 3.8 29.2 - - + +
165B VAL* 4.3 7.6 - - - +
167B THR* 3.8 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA 2.7 22.9 + - - -
55B ALA* 3.6 6.8 + - - -
57B ALA* 1.3 75.7 - - - +
59B SER* 1.4 62.6 + - - +
60B LYS 3.2 3.4 - - - -
61B GLY* 3.2 15.2 + - - -
64B VAL* 4.1 7.6 - - - -
77B LYS 5.0 1.0 + - - -
78B VAL* 4.2 17.9 - - - -
81B ALA* 3.5 32.5 - - - +
82B PRO* 5.6 1.4 - - - +
83B ILE* 4.0 11.2 - - - -
----------------------------------------------------------
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