Contacts of the helix formed by residues 81 - 91 (chain O) in PDB entry 3L73
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 81 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F GLU* 5.8 7.2 - - - -
103F GLU* 2.5 35.3 + - - -
76O THR* 3.8 11.7 - - - -
80O ALA* 1.3 76.6 - - - +
82O SER* 1.3 67.5 + - - +
83O PHE* 2.8 5.8 + - - -
84O ARG* 2.9 18.2 + - - +
85O ILE* 2.8 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 82 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289N HIS* 3.7 25.5 + - - -
74O PRO 3.1 26.6 + - - +
75O LEU* 4.3 5.5 - - - +
76O THR* 2.9 32.4 - - - +
81O SER* 1.3 70.4 - - - +
83O PHE* 1.3 62.0 + - - +
85O ILE* 4.1 1.6 - - - +
86O THR* 3.5 22.0 + - - -
136O GLU* 4.0 8.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F GLU* 4.1 17.3 - - + +
104F ARG* 3.5 50.9 - - + +
107F TRP* 3.7 25.4 - + + -
108F ASN* 4.1 5.4 - - - -
289N HIS* 3.3 36.2 + + + +
81O SER* 2.8 8.5 + - - +
82O SER* 1.3 78.7 - - - +
84O ARG* 1.3 69.4 + - - +
85O ILE 3.2 0.5 + - - -
86O THR* 3.3 2.8 + - - -
87O ARG* 2.9 76.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F GLU* 3.8 19.4 + - - +
107F TRP* 3.6 31.0 - - + -
79O GLY 3.1 17.4 + - - -
80O ALA* 3.2 33.6 - - - +
81O SER* 2.9 19.0 + - - +
83O PHE* 1.3 81.4 - - - +
85O ILE* 1.3 56.4 + - - +
87O ARG* 4.5 1.8 - - - -
88O GLY* 2.6 34.2 + - - +
121O GLU* 2.8 32.9 + - - -
122O TYR* 3.5 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73O SER 4.5 3.8 - - - +
74O PRO* 4.1 17.3 - - + +
75O LEU 3.5 24.7 - - - +
77O THR* 4.0 18.4 - - + +
80O ALA* 3.8 17.7 - - + +
81O SER 2.8 27.8 + - - +
82O SER 4.1 4.3 - - - +
84O ARG* 1.3 71.9 - - - +
86O THR* 1.3 66.0 + - - +
89O ILE* 3.1 29.1 + - + +
96O LEU* 4.3 19.5 - - + -
122O TYR* 3.6 25.1 - - + -
125O ASN* 5.9 0.2 - - + -
126O VAL* 4.5 7.0 - - + -
70V LEU* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286N GLY* 3.7 33.3 + - - -
289N HIS* 4.0 15.9 - - - +
290N LEU* 3.9 11.0 - - + -
74O PRO* 4.5 9.9 - - - +
82O SER 3.5 15.0 + - - -
83O PHE 3.3 3.1 + - - -
85O ILE* 1.3 74.8 - - - +
87O ARG* 1.3 66.7 + - - +
89O ILE* 4.1 0.7 - - - +
90O GLU* 3.1 46.3 + - - +
70V LEU* 4.0 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F TRP* 3.6 32.6 + - + +
108F ASN* 2.8 29.9 + - - +
288N LYS 5.4 1.6 + - - -
289N HIS* 2.8 26.0 + - - +
290N LEU 3.5 14.9 + - - -
291N SER* 3.4 24.1 + - - +
83O PHE* 2.9 58.5 + - + +
84O ARG* 4.3 0.9 - - - +
86O THR* 1.3 76.5 - - - +
88O GLY* 1.3 59.5 + - - +
90O GLU* 3.2 3.5 + - - +
91O ALA* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F TRP* 3.7 16.4 - - - -
84O ARG 2.6 24.2 + - - -
87O ARG* 1.3 75.2 - - - +
89O ILE* 1.3 60.3 + - - +
91O ALA* 3.3 15.6 - - - +
92O VAL* 4.0 9.4 + - - +
118O THR* 4.9 5.4 - - - +
122O TYR* 3.7 21.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 89 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85O ILE* 3.1 22.6 + - + +
86O THR 4.1 1.6 - - - +
88O GLY* 1.3 73.0 - - - +
90O GLU* 1.3 66.7 + - + +
91O ALA 3.1 0.2 - - - -
92O VAL* 3.2 14.6 - - - +
94O GLY* 2.9 48.6 + - - +
95O SER* 3.6 12.3 - - - +
96O LEU* 3.4 39.0 - - + -
109O VAL* 5.1 0.9 - - + -
119O VAL* 4.5 15.0 - - + -
122O TYR* 3.7 29.4 - - + -
70V LEU* 4.4 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289N HIS 4.3 0.3 - - - +
290N LEU* 3.6 19.7 - - - +
291N SER* 2.8 51.1 + - - +
292N SER 5.4 0.7 + - - -
356N ARG* 3.2 17.6 - - - +
360N HIS* 5.7 0.7 - - - +
86O THR* 3.1 30.2 + - + +
87O ARG 3.7 0.2 - - - +
89O ILE* 1.3 80.2 - - + +
91O ALA* 1.3 62.2 + - - +
92O VAL 3.1 0.4 - - - -
93O GLY* 3.1 15.1 + - - +
94O GLY 4.4 6.1 - - - +
70V LEU* 5.2 4.0 - - + -
71V ASN* 4.5 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107F TRP* 4.7 9.9 - - + +
355N LYS* 5.1 4.2 - - - +
356N ARG* 4.0 18.7 - - - +
359N ASN* 3.1 16.7 + - - -
87O ARG 2.8 13.1 + - - +
88O GLY* 3.3 17.9 - - - +
89O ILE 3.1 0.2 - - - -
90O GLU* 1.3 77.8 - - - +
92O VAL* 1.3 63.6 + - + +
----------------------------------------------------------
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