Contacts of the strand formed by residues 54 - 59 (chain F) in PDB entry 1M5P
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 GLN 54 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E G 3.1 38.9 - - + +
40E C 4.0 5.2 - - - +
13F TYR* 2.3 39.6 + - + +
14F ILE 3.1 13.7 - - - +
15F ASN* 3.9 1.1 - - + -
17F LEU* 3.6 5.3 - - - +
26F LEU* 4.9 1.1 - - - +
45F VAL* 4.2 16.8 - - - +
46F SER 4.5 0.5 + - - +
50F LYS 2.9 27.3 + - - -
51F MET* 3.2 31.7 - - + +
52F ARG 3.3 4.9 + - - -
53F GLY* 1.3 86.6 + - - +
55F ALA* 1.3 66.0 + - - +
56F PHE* 5.4 3.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
12F ILE 3.8 0.9 - - - +
13F TYR* 4.0 0.9 - - - -
14F ILE* 3.0 35.3 + - + +
17F LEU* 3.7 8.7 - - + -
30F LEU* 3.7 21.8 - - + -
43F ILE* 4.9 0.4 - - + -
44F LEU 3.4 7.2 - - - -
45F VAL* 3.5 24.0 - - + -
54F GLN* 1.3 79.2 - - - +
56F PHE* 1.3 69.1 + - - +
57F VAL* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E C 3.7 17.0 - - - -
41E A 3.2 78.5 - + + -
11F THR* 3.8 18.2 - - + -
12F ILE 3.7 3.4 - - - -
13F TYR* 3.7 32.3 - + + -
42F ASP 4.1 0.3 - - - +
43F ILE* 3.1 5.7 - - - +
44F LEU* 2.8 49.2 + - + +
51F MET* 3.8 13.7 - - + -
54F GLN* 5.4 1.1 - - + -
55F ALA* 1.3 82.1 - - - +
57F VAL* 1.3 62.2 + - - +
58F ILE* 4.0 1.6 - - + -
87F ALA* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F HIS 4.0 0.3 - - - +
11F THR* 3.5 2.3 - - - -
12F ILE* 3.1 42.8 + - + +
14F ILE* 4.0 19.1 - - + -
30F LEU* 4.6 10.1 - - + -
34F PHE* 4.7 7.2 - - + -
40F ILE* 4.1 25.6 - - + -
42F ASP 3.7 2.2 - - - -
43F ILE* 3.7 24.9 - - + -
55F ALA 5.0 0.4 - - - +
56F PHE* 1.3 79.6 - - - +
58F ILE* 1.3 62.4 + - - +
59F PHE* 3.8 26.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E A 5.3 0.2 - - - +
42E C 5.5 1.3 - - - +
10F HIS 4.5 1.1 - - - +
11F THR* 3.2 25.8 - - + +
40F ILE* 3.5 6.5 - - - +
41F LEU* 2.9 25.6 + - + -
42F ASP* 2.9 28.5 + - + +
44F LEU* 3.4 30.7 - - + -
56F PHE* 4.8 0.9 - - + -
57F VAL* 1.3 73.0 - - - +
59F PHE* 1.3 64.3 + - - +
91F SER* 3.9 19.5 - - - +
93F ILE* 3.6 32.8 - - + -
94F ILE* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F HIS* 2.9 33.7 + - - +
12F ILE* 3.7 26.0 - - + -
34F PHE* 3.8 22.4 - - + -
37F PHE* 4.0 8.7 - - + -
38F GLY 4.0 6.1 - - - -
39F GLN 3.7 14.6 - - - -
40F ILE* 3.8 19.5 - - + -
41F LEU* 4.4 2.7 - - - -
57F VAL* 4.0 18.2 - - + -
58F ILE* 1.3 75.2 - - - +
60F LYS* 1.3 63.6 + - - +
61F GLU 3.4 17.7 + - - +
64F SER* 3.8 13.5 - - - -
65F ALA* 3.7 18.8 - - + -
68F ALA* 3.7 25.1 - - + -
94F ILE* 4.1 5.0 - - - +
----------------------------------------------------------
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