Contacts of the helix formed by residues 84 - 93 (chain A) in PDB entry 1FS6
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 SER 84 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 3.7 15.9 - - - -
74A TYR* 4.4 1.6 - - - -
77A LEU* 3.5 25.6 - - - +
78A PRO 4.0 3.4 - - - -
79A LYS* 2.7 31.3 + - - -
81A HIS 3.2 1.9 + - - -
83A GLU* 1.3 83.2 - - - +
85A TYR* 1.3 63.6 + - - +
86A TYR* 3.5 2.6 + - - +
87A SER* 3.0 15.1 + - - -
88A PHE* 3.1 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.2 33.0 - - + -
70A ASN* 5.5 0.2 - - - +
72A ASP* 3.0 44.2 - - - +
73A GLU* 2.8 33.5 + - - +
74A TYR* 3.6 32.4 + + - -
83A GLU 4.7 2.0 - - - -
84A SER* 1.3 73.5 - - - +
86A TYR* 1.3 60.2 + - - +
88A PHE* 3.4 6.5 + - + +
89A MET* 2.9 35.3 + - - +
106A LEU* 4.4 4.9 - - + -
146A PHE* 3.3 34.0 - + - -
170A ASN* 4.5 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 3.0 16.4 + - - +
79A LYS* 3.2 62.1 - - + +
80A GLU* 4.7 11.7 - - + +
84A SER* 3.1 3.8 - - - +
85A TYR* 1.3 78.6 - - - +
87A SER* 1.3 68.5 + - - +
89A MET* 3.4 1.6 + - - +
90A HIS* 3.1 67.2 + + + -
106A LEU* 3.8 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LYS 3.0 14.4 + - - -
80A GLU* 3.7 6.8 + - - +
81A HIS 2.6 30.8 + - - -
82A PRO* 3.7 15.4 - - - +
84A SER* 3.0 10.4 + - - -
86A TYR* 1.3 82.2 - - - +
88A PHE* 1.3 65.5 + - - +
90A HIS* 4.2 2.5 - - - +
91A ARG* 3.0 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.5 31.4 - - + -
42A GLY* 3.2 41.1 - - - -
46A MET* 3.6 18.4 - - - -
49A TYR* 3.8 26.7 - + - -
83A GLU* 5.9 0.9 - - - +
84A SER 3.1 13.1 + - - +
85A TYR* 3.7 12.6 - + + +
87A SER* 1.3 75.1 - - - +
89A MET* 1.3 63.6 + - - +
91A ARG* 3.6 17.4 - - - +
92A ASN* 2.8 58.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.6 16.8 - - + -
40A PRO 3.9 1.1 - - - +
41A THR* 3.6 14.4 - - + -
49A TYR* 3.5 34.1 - - + +
70A ASN* 3.2 42.8 - - - +
85A TYR 2.9 21.7 + - - +
86A TYR* 3.7 5.2 - - - +
87A SER 3.2 0.2 - - - -
88A PHE* 1.3 84.7 - - - +
90A HIS* 1.3 57.5 + - - +
92A ASN* 5.1 0.2 - - - -
93A PHE* 2.9 32.6 + - + +
94A PHE* 3.0 36.9 + - + -
106A LEU* 4.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 3.1 67.5 + + + +
87A SER* 4.2 3.4 - - - +
89A MET* 1.3 73.9 - - - +
91A ARG* 1.3 66.5 + - - +
92A ASN 3.3 0.7 + - - -
93A PHE 3.4 1.9 + - - -
94A PHE* 3.3 36.8 - + + +
95A ASP* 2.8 44.1 + - - +
104A ILE* 4.0 15.9 - - + +
106A LEU* 4.6 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PRO* 2.7 38.3 + - - +
83A GLU* 4.5 8.9 + - - -
87A SER* 3.0 27.2 + - - +
88A PHE* 3.6 23.4 - - - +
90A HIS* 1.3 78.2 - - - +
92A ASN* 1.3 71.0 + - - +
95A ASP* 3.6 11.2 + - - +
96A HIS* 2.7 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A MET* 3.0 33.3 - - + +
49A TYR* 3.6 19.4 - - + +
50A LYS* 5.0 0.3 + - - -
53A VAL* 4.1 10.4 - - - +
88A PHE* 2.8 59.8 + - + +
89A MET 4.6 0.4 - - - +
91A ARG* 1.3 95.8 - - - +
93A PHE* 1.3 60.7 + - + +
96A HIS* 4.0 5.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 5.3 3.4 - - + -
39A LEU* 4.2 12.3 - - + -
49A TYR* 3.8 32.1 - + + -
52A LEU* 3.9 28.3 - - + -
53A VAL* 4.1 10.1 - - + -
63A PHE* 3.8 34.3 - + - -
68A THR* 5.0 4.7 - - + -
89A MET* 2.9 18.2 + - + +
90A HIS 3.4 2.0 + - - -
92A ASN* 1.3 81.3 - - + +
94A PHE* 1.3 94.2 + + - +
95A ASP 3.2 1.6 - - - -
96A HIS* 3.0 16.4 + - - +
97A VAL* 3.4 38.6 + - + +
99A ILE* 5.7 1.6 - - + -
----------------------------------------------------------
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