Contacts of the helix formed by residues 83 - 95 (chain I) in PDB entry 1O1F
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 83 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786G ILE* 6.0 2.2 - - + -
80I ASP 5.2 3.8 - - - +
81I GLN* 3.1 15.7 + - - +
82I GLY* 1.3 72.5 - - - +
84I PHE* 1.3 64.2 + - - +
85I GLU* 3.2 15.6 + - - +
86I ASP* 3.1 38.3 + - + +
87I PHE* 3.4 18.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I GLY 3.8 3.5 + - - -
83I THR* 1.3 71.0 + - - +
85I GLU* 1.3 94.0 + - - +
87I PHE* 3.3 11.9 + - + +
88I VAL* 3.2 35.5 + - + +
143I VAL* 5.4 0.2 - - + -
147I MET* 3.6 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I THR* 3.2 11.9 + - - +
84I PHE* 1.3 113.1 - - - +
86I ASP* 1.3 63.2 + - - +
88I VAL* 3.3 3.3 + - - +
89I GLU* 2.9 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786G ILE* 3.7 40.3 - - + +
83I THR* 3.1 36.0 + - + +
85I GLU* 1.3 81.2 - - - +
87I PHE* 1.3 61.5 + - + +
89I GLU* 3.6 11.9 - - - +
90I GLY* 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786G ILE* 3.4 23.1 - - + -
789G ALA* 4.5 4.5 - - + -
790G THR* 1.9 48.7 - - + -
793G ARG* 6.4 1.8 - - + -
81I GLN 4.4 3.8 - - - -
82I GLY* 4.0 14.1 - - - -
83I THR* 3.4 35.9 - - + -
84I PHE* 3.3 15.0 + - - +
85I GLU 3.3 0.4 - - - -
86I ASP* 1.3 83.5 - - + +
88I VAL* 1.3 62.5 + - - +
90I GLY* 3.4 6.6 + - - -
91I LEU* 3.4 22.4 + - + +
143I VAL* 4.2 15.7 - - + -
147I MET* 4.0 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I PHE* 3.2 24.9 + - + +
85I GLU* 4.0 3.6 - - - +
87I PHE* 1.3 77.2 - - - +
89I GLU* 1.3 59.6 + - + +
91I LEU* 3.4 6.3 + - - +
92I ARG* 2.9 32.5 + - + +
139I TYR* 4.1 17.6 - - + +
140I GLU* 5.3 12.6 - - + +
143I VAL* 4.0 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I GLU* 2.9 47.0 + - - +
86I ASP* 3.6 13.7 - - - +
88I VAL* 1.3 76.7 - - + +
90I GLY* 1.3 66.0 + - - +
92I ARG* 3.2 7.9 + - + +
93I VAL* 3.0 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 90 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786G ILE* 6.4 1.1 - - - -
86I ASP 2.9 17.4 + - - -
87I PHE* 3.4 2.2 + - - -
88I VAL 3.3 0.4 - - - -
89I GLU* 1.3 79.0 - - - +
91I LEU* 1.3 62.0 + - - +
93I VAL* 3.2 14.7 + - - +
94I PHE* 3.3 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I PHE 3.4 10.4 + - - +
88I VAL 3.4 4.5 + - - +
90I GLY* 1.3 76.2 - - - +
92I ARG* 1.3 57.2 + - - +
94I PHE* 3.1 34.2 + - + +
95I ASP* 2.9 24.4 - - - +
102I VAL* 4.5 6.1 - - + -
107I LEU* 4.7 10.3 - - + -
139I TYR* 3.1 34.3 + - + -
142I PHE* 4.5 12.3 - - + -
143I VAL* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88I VAL* 2.9 23.2 + - + +
89I GLU* 3.2 10.9 + - + +
91I LEU* 1.3 76.9 - - - +
93I VAL* 1.3 60.3 + - + +
94I PHE 3.2 0.2 - - - -
95I ASP 3.2 21.2 - - - +
97I GLU 4.8 8.7 - - - -
98I GLY* 3.9 9.1 - - - -
99I ASN* 3.7 21.3 - - - +
100I GLY* 3.7 21.7 - - - +
139I TYR* 3.0 23.9 + - - +
140I GLU* 3.8 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779G ARG* 5.2 12.6 - - - +
89I GLU* 3.0 17.6 + - + +
90I GLY* 3.2 9.8 + - - +
92I ARG* 1.3 78.6 - - + +
94I PHE* 1.3 60.7 + - - +
95I ASP 3.4 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749G GLY 3.5 24.7 - - - -
750G GLY* 4.3 3.6 - - - -
751G GLY 5.1 5.8 - - - -
755G HIS* 5.8 4.3 - + - -
90I GLY 3.3 10.9 + - - +
91I LEU* 3.1 26.6 + - + +
93I VAL* 1.3 80.2 - - - +
95I ASP* 1.3 59.1 + - - +
102I VAL* 3.6 39.5 - - + -
106I GLU* 3.8 29.9 - - + +
107I LEU* 4.3 5.2 - - + -
110I VAL* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 95 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91I LEU 2.9 8.5 + - - +
92I ARG* 3.2 14.7 - - - +
93I VAL 3.4 1.7 - - - -
94I PHE* 1.3 82.9 - - + +
96I LYS* 1.3 78.6 + - - +
97I GLU 4.1 3.8 - - - +
99I ASN 3.7 6.4 - - - +
101I THR 3.1 30.4 + - - +
102I VAL* 3.4 16.1 - - - +
103I MET 5.6 0.2 - - - +
106I GLU* 5.1 4.9 - - - +
139I TYR* 2.8 43.5 + - - -
----------------------------------------------------------
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