Contacts of the helix formed by residues 84 - 93 (chain W) in PDB entry 1I84
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 CYS 84 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82W GLN 4.9 3.6 - - - -
83W GLY* 1.3 77.4 - - - +
85W PHE* 1.3 72.2 + - - +
86W GLU* 3.5 23.8 - - - +
87W ASP* 2.7 38.2 + - - +
88W TYR* 2.7 24.3 + - - +
148W LEU* 4.6 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84W CYS* 1.3 70.6 - - - +
86W GLU* 1.3 87.0 + - - +
87W ASP 2.6 1.6 + - - -
88W TYR* 2.9 12.1 + - - -
89W VAL* 3.0 32.7 + - + +
141W GLU* 3.0 42.6 - - - -
144W VAL* 3.1 22.4 - - + -
145W ARG* 2.9 57.0 - - + -
148W LEU* 3.9 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84W CYS* 2.8 24.6 + - - +
85W PHE* 1.3 98.3 + - - +
87W ASP* 1.3 64.1 + - - +
89W VAL* 4.7 2.6 - - - +
90W GLU* 3.5 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795V VAL* 4.1 8.7 - - + +
83W GLY* 6.2 1.3 - - - -
84W CYS* 2.7 30.4 + - - +
85W PHE 2.6 3.8 + - - -
86W GLU* 1.3 77.8 - - - +
88W TYR* 1.3 69.4 + - - +
89W VAL 3.3 0.2 - - - -
90W GLU* 2.8 47.3 + - - +
91W GLY 3.1 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795V VAL* 4.4 13.7 - - + +
798V ALA* 3.2 20.7 + - + +
799V PHE* 3.2 45.4 - + + +
802V GLN* 2.5 52.7 + - + +
83W GLY* 3.2 14.6 + - - -
84W CYS* 2.7 43.4 + - - +
85W PHE* 2.9 4.4 + - - +
87W ASP* 1.3 75.5 - - - +
89W VAL* 1.3 63.7 + - + +
91W GLY* 3.2 8.1 + - - -
92W LEU* 3.7 13.4 + - - +
144W VAL* 4.7 9.6 - - + -
148W LEU* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85W PHE* 3.0 40.6 + - + +
86W GLU* 4.7 3.1 - - - +
88W TYR* 1.3 69.8 - - - +
90W GLU* 1.3 70.1 + - - +
91W GLY 2.8 7.5 + - - -
92W LEU* 2.8 16.7 + - - +
93W ARG* 2.8 17.2 + - + +
140W TYR* 4.5 13.1 - - + -
141W GLU* 4.5 12.6 - - - +
144W VAL* 3.3 43.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795V VAL* 4.4 10.4 - - - +
86W GLU 3.5 14.4 - - - +
87W ASP* 2.8 50.8 + - - +
89W VAL* 1.3 81.0 - - - +
91W GLY* 1.3 61.7 + - - +
93W ARG* 4.1 12.0 + - - +
94W VAL* 3.4 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 91 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736V ILE* 6.1 0.2 - - - -
792V ILE* 4.8 13.6 - - - +
795V VAL* 4.8 11.7 - - - -
796V ILE* 5.5 2.5 - - - -
87W ASP 3.1 8.6 + - - -
88W TYR 3.2 4.6 + - - -
89W VAL 2.8 1.8 + - - -
90W GLU* 1.3 82.4 - - - +
92W LEU* 1.3 68.0 + - - +
93W ARG 3.3 0.2 - - - -
94W VAL* 3.1 24.3 - - - +
95W PHE* 3.9 9.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796V ILE* 4.3 21.5 - - + -
799V PHE* 4.4 29.4 - - + -
88W TYR 3.7 13.0 + - - +
89W VAL* 2.8 11.2 + - - +
91W GLY* 1.3 71.2 - - - +
93W ARG* 1.3 52.4 + - - +
94W VAL 2.7 17.2 + - - -
95W PHE* 2.7 33.0 + - + +
96W ASP 3.8 1.7 + - - -
103W VAL* 4.3 5.9 - - + +
108W ILE* 3.8 31.2 - - + -
111W VAL* 5.5 0.7 - - + -
112W LEU* 5.3 2.7 - - + -
140W TYR* 4.0 30.5 - - + -
143W LEU* 4.6 7.2 - - + -
144W VAL* 4.8 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732V GLN* 4.1 7.5 + - - +
89W VAL* 2.8 17.4 + - + +
90W GLU* 4.1 10.3 - - - +
91W GLY 3.3 0.4 - - - -
92W LEU* 1.3 75.3 - - - +
94W VAL* 1.3 56.0 + - + +
95W PHE 3.2 2.2 - - - -
96W ASP* 3.4 23.6 + - + +
99W GLY* 5.1 14.7 + - - -
101W GLY* 5.4 2.6 - - - -
140W TYR* 3.5 39.8 + - + +
141W GLU* 5.1 5.6 + - - -
----------------------------------------------------------
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