Contacts of the helix formed by residues 68 - 79 (chain A) in PDB entry 1FX8
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 ASN 68 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A HIS* 2.9 9.7 + - - +
67A LEU* 1.3 82.1 - - - +
69A PRO* 1.3 71.4 - - - +
70A ALA* 2.9 17.5 + - - +
71A VAL* 3.0 18.3 + - + +
72A THR* 3.0 21.3 + - - -
93A GLN* 3.3 7.7 - - - -
156A THR* 5.5 0.6 - - - +
159A LEU* 4.3 4.0 - - - +
202A MET 2.9 22.8 + - - -
203A ASN* 3.2 15.4 - - - +
204A PRO* 3.4 13.5 - - - +
663A GOL 3.1 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 1.3 85.9 - - - +
70A ALA* 1.3 61.4 + - - +
72A THR* 3.3 2.0 + - - -
73A ILE* 3.0 34.0 + - + +
90A ILE* 4.1 32.1 - - + -
93A GLN* 3.0 18.6 - - - +
94A VAL* 4.8 1.8 - - + -
203A ASN* 3.3 17.9 - - - +
204A PRO* 3.9 15.7 - - + -
205A ALA* 3.5 28.0 - - + +
241A ILE* 5.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 2.9 14.0 + - - +
69A PRO* 1.3 78.0 - - - +
71A VAL* 1.3 58.2 + - + +
73A ILE* 3.7 3.5 + - - +
74A ALA* 3.1 28.6 + - - +
156A THR* 4.5 1.8 - - + -
202A MET 4.5 2.2 - - - +
204A PRO* 3.9 8.8 - - + +
240A PRO* 3.7 35.4 - - + +
241A ILE* 3.9 12.9 - - - +
244A ALA* 3.5 13.0 - - + +
245A ILE* 5.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA 5.5 0.2 - - - +
66A HIS* 4.2 18.4 - - + +
68A ASN* 3.0 32.8 + - + +
70A ALA* 1.3 77.8 - - + +
72A THR* 1.3 59.6 + - - +
74A ALA* 3.3 1.0 + - - +
75A LEU* 2.9 55.8 + - + +
156A THR* 6.3 0.7 - - + -
159A LEU* 5.2 3.8 - - + -
160A MET* 4.0 27.6 - - + -
163A ILE* 4.5 15.5 - - + -
244A ALA* 5.5 1.3 - - + -
663A GOL 4.0 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A HIS* 2.6 30.7 + - - +
68A ASN 3.0 6.9 + - - -
69A PRO* 3.6 9.6 - - - -
71A VAL* 1.3 78.1 - - - +
73A ILE* 1.3 63.5 + - - +
75A LEU* 3.3 2.6 + - - +
76A TRP* 3.0 21.0 + - - +
81A PHE* 4.0 11.3 - - + -
86A VAL* 3.9 40.6 - - + +
89A PHE* 3.9 4.4 - - + -
90A ILE* 4.4 2.7 - - + -
93A GLN* 3.1 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO* 3.0 21.7 + - + +
70A ALA* 4.0 4.3 - - - +
72A THR* 1.3 75.7 - - - +
74A ALA* 1.3 58.7 + - - +
76A TRP* 3.2 20.7 + - + +
77A LEU* 3.0 43.9 + - + +
86A VAL* 4.5 7.6 - - + -
90A ILE* 4.0 22.4 - - + -
241A ILE* 4.1 41.3 - - + -
245A ILE* 4.5 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA 3.1 19.9 + - - +
71A VAL 3.8 3.1 - - - +
73A ILE* 1.3 77.5 - - - +
75A LEU* 1.3 60.1 + - - +
77A LEU* 3.3 1.5 + - - +
78A PHE* 2.8 39.9 + - - +
160A MET* 3.9 16.6 - - + -
244A ALA* 3.9 26.5 - - + +
245A ILE* 4.4 6.5 - - + +
248A ALA* 4.3 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A HIS* 3.4 35.7 - - + +
71A VAL* 2.9 36.1 + - + +
72A THR 3.8 4.0 - - - +
74A ALA* 1.3 76.5 - - - +
76A TRP* 1.3 57.5 + - - +
79A ALA* 2.8 41.5 + - + +
81A PHE* 3.0 26.1 + - + -
160A MET* 4.2 19.7 - - + -
163A ILE* 6.4 0.2 - - + -
164A LEU* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR 3.0 13.4 + - - +
73A ILE* 3.3 27.4 - - + +
75A LEU* 1.3 80.8 - - - +
77A LEU* 1.3 89.3 + - + +
78A PHE 3.7 0.2 + - - -
80A CYS* 4.1 9.9 + - - -
81A PHE* 3.4 26.6 + - + +
83A LYS* 3.1 37.8 - - + +
86A VAL* 3.8 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.0 24.5 + - + +
74A ALA 3.3 0.2 + - - -
76A TRP* 1.3 113.6 - - + +
78A PHE* 1.3 83.3 + - + +
79A ALA 3.9 0.2 - - - -
80A CYS 5.3 0.4 - - - -
245A ILE* 3.7 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA 2.8 23.7 + - - +
77A LEU* 1.3 94.2 - - + +
79A ALA* 1.3 59.3 + - - +
80A CYS* 3.8 2.2 - - - -
164A LEU* 6.0 0.2 - - + -
245A ILE* 3.6 47.6 - - + -
248A ALA* 3.6 20.6 - - + -
249A PHE* 3.9 36.1 - + + -
252A ARG* 2.8 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 2.8 39.7 + - + +
78A PHE* 1.3 79.4 - - - +
80A CYS* 1.3 75.5 + - - +
81A PHE* 3.2 3.3 + - + -
164A LEU* 5.8 0.2 - - + -
252A ARG* 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