Contacts of the helix formed by residues 41 - 55 (chain F) in PDB entry 4OA5
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 GLY 41 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F ASN* 5.9 0.4 - - - -
28F HIS* 4.4 6.1 - - - -
39F GLN 3.6 1.6 + - - -
40F LEU* 1.3 75.8 - - - +
42F THR* 1.3 60.7 + - - -
43F VAL 3.3 2.7 - - - -
44F GLU* 3.1 20.7 + - - -
45F GLY 2.9 23.7 + - - -
69F PHE* 3.6 7.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F ASN* 3.0 25.1 + - - -
18F ALA* 3.5 9.2 - - - +
19F VAL* 3.0 48.1 + - + +
25F LEU* 3.6 23.1 - - + -
28F HIS* 5.6 4.0 - - + -
41F GLY* 1.3 69.6 - - - -
43F VAL* 1.3 63.8 + - - +
45F GLY 3.4 0.2 + - - -
46F GLN 3.2 12.3 + - - -
69F PHE* 4.1 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR* 5.0 11.4 + - + -
204A ILE 5.9 0.7 - - - +
13F LEU* 3.6 53.2 - - + +
14F ASN* 3.7 23.5 + - - +
17F PHE* 3.8 14.9 - - + +
18F ALA* 3.9 3.4 - - + -
41F GLY 3.3 0.6 - - - -
42F THR* 1.3 75.3 + - - +
44F GLU* 1.3 78.1 + - + +
46F GLN* 3.2 5.2 + - - +
47F MET* 3.1 19.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F LEU* 4.1 25.1 - - + -
41F GLY* 3.1 29.1 + - - +
43F VAL* 1.3 89.9 + - + +
45F GLY* 1.3 63.1 + - - +
47F MET* 3.2 14.7 + - + +
48F LEU* 3.0 25.5 + - - +
162F ASP* 5.7 1.3 - - - +
207F THR* 4.5 25.7 - - + +
209F GLU* 4.6 12.4 - - - +
211F MET* 4.6 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 45 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F VAL* 3.8 6.1 - - - -
40F LEU* 4.2 11.8 - - - +
41F GLY 2.9 16.9 + - - -
42F THR 3.4 3.1 + - - -
43F VAL 3.2 0.2 - - - -
44F GLU* 1.3 77.2 - - - +
46F GLN* 1.3 60.1 + - - +
48F LEU* 3.4 5.8 + - - +
49F GLN* 3.2 24.3 + - - +
69F PHE* 4.9 0.4 - - - -
73F CYS* 4.1 23.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LYS* 3.0 32.2 + - - +
201A LEU* 3.9 19.0 - - + +
202A SER 2.8 35.9 + - - +
203A THR* 4.2 0.7 - - - +
16F LEU 4.7 0.2 + - - -
17F PHE* 3.4 36.6 - - - +
18F ALA 3.2 8.0 - - - -
19F VAL* 3.5 8.2 + - + +
42F THR 3.2 10.4 + - - +
43F VAL 3.2 3.1 + - - +
45F GLY* 1.3 74.7 - - - +
47F MET* 1.3 59.1 + - - +
49F GLN* 3.1 15.3 + - - +
50F LEU* 2.9 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 47 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A THR* 3.5 35.3 + - + +
205A ILE* 5.3 4.7 - - + -
206A PRO* 5.4 2.5 - - - -
43F VAL* 3.1 13.0 + - + +
44F GLU* 3.2 15.2 + - - +
46F GLN* 1.3 76.1 - - - +
48F LEU* 1.3 63.5 + - + +
50F LEU* 3.2 8.3 + - + +
51F LEU* 3.0 34.2 + - + +
205F ILE* 3.7 32.5 - - + -
207F THR* 4.4 11.7 - - + -
211F MET* 3.8 43.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F LEU* 3.4 26.2 - - + -
44F GLU 3.0 16.2 + - - +
45F GLY* 3.6 8.5 - - - +
46F GLN 3.3 0.2 - - - -
47F MET* 1.3 75.9 - - + +
49F GLN* 1.3 60.6 + - - +
51F LEU* 3.2 13.8 + - + +
52F ILE* 2.9 35.8 + - + +
70F SER* 4.7 3.4 - - - +
73F CYS* 6.0 0.2 - - + -
74F MET* 3.9 34.8 - - + -
132F MET* 4.8 6.5 - - + +
134F PHE* 4.1 18.4 - - + -
160F VAL* 3.9 28.3 - - + -
211F MET* 4.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 49 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 3.8 17.4 - - + +
19F VAL* 3.7 25.7 - - - +
21F THR* 6.2 1.2 - - - +
45F GLY 3.2 8.5 + - - +
46F GLN* 3.1 24.8 + - - +
48F LEU* 1.3 75.8 - - - +
50F LEU* 1.3 58.1 + - - +
52F ILE* 3.3 4.2 + - - +
53F ARG* 2.9 33.1 + - - +
73F CYS* 2.9 36.1 + - - +
74F MET 4.7 0.2 - - - +
76F HIS* 3.9 17.1 + - - +
77F ALA* 3.7 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 3.3 36.9 - - + +
202A SER 5.5 0.2 - - - -
203A THR* 3.7 22.9 - - - +
205A ILE* 6.4 0.7 - - + -
213A VAL* 3.6 36.1 - - + +
215A ILE* 3.5 27.6 - - + +
46F GLN 2.9 13.3 + - - +
47F MET* 3.4 12.3 - - + +
48F LEU 3.2 0.2 - - - -
49F GLN* 1.3 76.3 - - - +
51F LEU* 1.3 60.2 + - + +
53F ARG* 3.3 1.2 + - - +
54F MET* 2.8 46.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 6.1 0.2 - - + -
51A LEU* 5.3 6.5 - - + -
54A MET* 3.6 32.3 - - + +
47F MET* 3.0 30.6 + - + +
48F LEU* 3.2 25.3 + - + +
50F LEU* 1.3 79.7 - - + +
52F ILE* 1.3 63.8 + - + +
54F MET* 3.3 7.5 + - - -
55F ALA* 3.0 28.2 + - - +
132F MET* 5.6 1.6 - - + -
158F LEU* 4.3 8.5 - - + +
160F VAL* 4.4 10.1 - - + -
205F ILE* 6.3 2.2 - - + -
213F VAL* 3.7 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LEU 2.9 21.8 + - - +
49F GLN* 3.6 5.2 - - - +
51F LEU* 1.3 76.1 - - - +
53F ARG* 1.3 60.4 + - - +
56F GLY* 3.2 3.6 + - - -
57F ILE* 3.1 39.3 + - + +
60F ILE* 3.6 12.3 - - + -
74F MET* 3.5 47.3 - - + +
77F ALA* 3.8 21.3 - - + +
78F LEU* 3.8 23.6 - - + -
79F PRO* 5.6 0.2 - - + -
132F MET* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 3.6 16.8 - - + +
215A ILE* 3.3 21.6 - - + +
217A LEU* 3.5 31.3 - - - +
49F GLN 2.9 19.5 + - - +
52F ILE* 1.3 74.2 - - - +
54F MET* 1.3 66.8 + - - +
56F GLY* 3.3 10.5 + - - -
76F HIS 4.5 5.1 + - - -
77F ALA* 3.4 35.1 + - + +
78F LEU 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 54 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.6 48.0 - - + +
54A MET* 3.5 18.2 - - + +
55A ALA* 3.4 24.8 - - + +
158A LEU* 3.8 22.0 - - + -
213A VAL* 4.0 17.0 - - - -
215A ILE* 3.6 22.0 - - + -
50F LEU* 2.8 41.4 + - - +
51F LEU* 3.7 6.3 - - - +
53F ARG* 1.3 74.8 - - - +
55F ALA* 1.3 60.9 + - - +
56F GLY 3.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A MET* 3.4 25.8 - - + +
51F LEU 3.0 16.4 + - - +
54F MET* 1.3 76.0 - - - +
56F GLY* 1.3 63.3 + - - +
57F ILE* 3.3 23.4 + - + +
154F ARG* 4.4 9.6 + - - +
158F LEU* 3.9 15.9 - - + -
----------------------------------------------------------
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