Contacts of the helix formed by residues 102 - 113 (chain O) in PDB entry 5A15
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 GLU 102 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O ASP* 5.4 0.2 - - - +
81O LEU* 3.9 14.0 - - + +
100O PHE* 3.3 28.1 - - + -
101O PRO* 1.3 94.6 - - + +
103O LYS* 1.3 63.8 + - - +
104O GLY 3.3 2.7 - - - +
105O ARG* 3.1 47.9 + - + +
106O LEU* 3.3 14.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 103 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96O LEU* 4.4 19.3 - - + -
99O HIS 6.2 0.2 - - - -
100O PHE* 3.2 31.4 + - + +
101O PRO* 3.7 12.1 + - - +
102O GLU* 1.3 77.5 - - - +
104O GLY* 1.3 62.7 + - - +
106O LEU* 3.5 5.3 + - - +
107O LYS* 3.2 21.1 + - - +
122O LEU* 4.8 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 104 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O GLU* 3.3 0.8 - - - +
103O LYS* 1.3 77.8 - - - +
105O ARG* 1.3 63.8 + - - +
107O LYS* 3.4 11.5 + - - +
108O ARG* 3.1 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O ASP* 3.6 29.7 + - - +
81O LEU* 3.6 18.8 - - + +
102O GLU* 3.1 43.7 + - + +
103O LYS 3.4 0.4 - - - -
104O GLY* 1.3 74.0 - - - +
106O LEU* 1.3 62.1 + - - +
108O ARG* 3.0 11.2 + - - +
109O GLU* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81O LEU* 3.5 41.8 - - + +
84O TYR* 4.0 23.1 - - + -
85O ILE* 3.9 16.8 - - + +
94O VAL* 5.8 2.7 - - + -
96O LEU* 4.1 28.0 - - + -
100O PHE* 4.3 8.3 - - + -
102O GLU 3.3 16.0 + - - +
103O LYS 3.8 4.9 - - - +
105O ARG* 1.3 79.2 - - - +
107O LYS* 1.3 57.5 + - - +
109O GLU* 3.3 2.2 + - + +
110O ALA* 3.0 26.9 + - - +
118O LEU* 5.9 1.6 - - + -
122O LEU* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O LYS 3.2 11.5 + - - +
104O GLY* 3.4 13.2 + - - +
105O ARG 3.2 0.4 - - - -
106O LEU* 1.3 79.6 - - - +
108O ARG* 1.3 61.4 + - - +
110O ALA* 3.3 3.7 + - - +
111O GLU* 2.8 51.4 + - - +
119O VAL* 4.1 13.7 - - + +
122O LEU* 3.5 29.3 - - + +
123O THR* 3.4 33.4 - - + -
124O PRO* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77O ARG* 4.1 19.5 - - - +
104O GLY 3.1 12.6 + - - +
105O ARG* 3.0 13.3 + - - +
107O LYS* 1.3 75.6 - - - +
109O GLU* 1.3 65.8 + - - +
111O GLU* 3.3 36.8 + - - +
112O TYR* 3.1 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77O ARG* 2.9 50.8 + - - +
78O ASP* 4.0 22.7 + - - +
81O LEU* 3.7 25.3 - - + +
85O ILE* 4.3 15.7 - - + -
105O ARG* 2.9 22.0 + - - +
106O LEU* 3.6 8.1 - - - +
108O ARG* 1.3 74.6 - - - +
110O ALA* 1.3 67.1 + - - +
112O TYR* 3.2 2.1 + - - +
113O PHE* 3.0 39.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85O ILE* 3.9 9.1 - - + +
106O LEU 3.0 13.9 + - - +
107O LYS 3.5 9.6 - - - +
109O GLU* 1.3 75.1 - - - +
111O GLU* 1.3 58.8 + - - +
113O PHE* 3.5 3.6 + - - +
114O GLN 3.0 20.8 + - - -
115O LEU* 3.0 14.8 + - - +
118O LEU* 3.8 32.3 - - + -
119O VAL* 3.6 17.3 - - + +
122O LEU* 4.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107O LYS* 2.8 52.1 + - - +
108O ARG* 3.4 36.7 + - - +
109O GLU 3.2 0.2 - - - -
110O ALA* 1.3 74.4 - - - +
112O TYR* 1.3 60.2 + - - +
114O GLN* 2.9 25.7 + - - +
119O VAL* 3.6 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 112 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O LEU* 3.4 35.8 - - + +
75O ILE* 5.0 4.4 - - + +
76O ASP* 5.1 3.6 + - - +
77O ARG* 3.4 64.7 - - + +
108O ARG* 3.1 28.5 + - - +
109O GLU 3.2 6.9 + - - +
111O GLU* 1.3 78.8 - - - +
113O PHE* 1.3 77.2 + + - +
114O GLN* 3.2 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O SER* 3.8 4.3 - - - -
50O LEU* 3.0 37.1 + - + -
51O LEU* 3.7 37.4 + - + -
54O MET* 6.1 0.4 - - - -
75O ILE* 4.1 24.0 - - + -
77O ARG* 4.4 4.5 - - + -
82O PHE* 3.7 33.0 - + + -
85O ILE* 4.1 20.0 - - + -
109O GLU* 3.0 44.1 + - + +
110O ALA 4.1 3.4 - - - +
112O TYR* 1.3 85.8 - + - +
114O GLN* 1.3 67.6 + - - +
115O LEU* 3.7 16.9 + - + +
----------------------------------------------------------
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