Contacts of the helix formed by residues 74 - 84 (chain A) in PDB entry 5FQU
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 THR 74 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 5.2 0.2 - - - -
72A GLY 3.5 5.4 + - - +
73A TYR* 1.3 75.5 - - - +
75A PRO* 1.3 76.5 - - + +
76A ALA* 4.1 8.5 + - - +
77A GLU* 2.9 34.4 + - - +
78A LEU* 3.0 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 3.7 7.6 - - + +
43A LEU* 3.8 26.7 - - + +
44A LYS* 3.6 31.2 - - + +
47A ASP* 3.4 29.6 - - + +
69A TYR* 4.0 9.4 - - + -
74A THR* 1.3 86.7 - - + +
76A ALA* 1.3 52.5 + - + +
78A LEU* 3.2 15.7 + - + +
79A GLU* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS* 5.2 5.5 - - + +
74A THR* 4.2 8.5 - - - +
75A PRO* 1.3 77.7 - - - +
77A GLU* 1.3 60.5 + - - +
79A GLU* 3.5 12.2 + - - +
80A ARG* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 3.7 27.7 - - + -
74A THR* 2.9 21.9 + - - +
76A ALA* 1.3 77.3 - - - +
78A LEU* 1.3 65.5 + - - +
80A ARG* 2.4 43.8 + - - +
81A ILE* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 4.0 16.8 - - + +
43A LEU* 4.0 22.0 - - + -
65A VAL* 4.0 26.0 - - + +
68A LEU* 3.6 37.7 - - + -
69A TYR* 4.2 10.3 - - + +
73A TYR* 3.8 17.0 - - + -
74A THR 3.0 17.5 + - - +
75A PRO* 3.4 12.1 - - + +
77A GLU* 1.3 78.4 - - - +
79A GLU* 1.3 56.9 + - - +
81A ILE* 3.4 9.4 + - + +
82A ALA* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 4.1 11.8 - - + +
44A LYS* 2.8 40.4 + - - +
75A PRO 2.8 16.1 + - - +
76A ALA* 3.6 9.2 - - - +
77A GLU 3.2 0.2 - - - -
78A LEU* 1.3 74.5 - - - +
80A ARG* 1.3 64.5 + - - +
82A ALA* 3.2 3.2 + - - +
83A LEU* 3.0 44.8 + - + +
294A ILE* 3.8 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA 3.0 16.5 + - - +
77A GLU* 2.4 42.9 + - - +
79A GLU* 1.3 76.4 - - - +
81A ILE* 1.3 70.3 + - - +
83A LEU* 3.4 6.6 + - - -
84A GLU* 3.1 65.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 6.1 2.7 - - + -
73A TYR* 3.7 23.8 - - + +
77A GLU* 3.0 34.3 + - - +
78A LEU* 3.7 9.9 - - + +
80A ARG* 1.3 83.6 - - - +
82A ALA* 1.3 65.3 + - + +
84A GLU* 3.4 11.2 + - - -
85A MSE 3.6 28.5 - - + +
87A TRP* 6.5 0.2 - - + -
144A LEU* 3.7 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 4.3 13.0 - - + -
40A ILE* 4.1 16.8 - - + -
78A LEU 3.0 17.4 + - - +
79A GLU* 3.2 5.4 + - - +
81A ILE* 1.3 80.5 - - - +
83A LEU* 1.3 60.1 + - - +
84A GLU 3.5 0.5 + - - -
85A MSE 4.3 2.1 + - - +
87A TRP* 3.4 33.4 + - + -
290A VAL* 4.1 23.6 - - + +
294A ILE* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.0 43.3 + - + +
80A ARG* 3.4 7.6 + - - +
81A ILE 3.3 0.2 - - - -
82A ALA* 1.3 76.1 - - - +
84A GLU* 1.3 63.7 + - + +
85A MSE 3.8 1.5 + - - -
290A VAL* 3.7 27.6 - - + -
291A PRO* 3.9 27.6 - - + -
294A ILE* 4.6 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 3.1 56.5 + - + +
81A ILE* 3.4 4.0 + - - +
82A ALA 3.3 0.8 - - - -
83A LEU* 1.3 85.0 - - + +
85A MSE 1.3 59.3 + - - +
----------------------------------------------------------
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