Contacts of the helix formed by residues 120 - 132 (chain O) in PDB entry 5OXV
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 MET 120 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242I C 5.9 1.3 - - - +
-238J A 3.6 41.7 - - - +
-237J C 3.9 13.9 - - - +
107O THR* 4.7 0.2 - - - +
116O ARG* 3.8 27.4 - - - +
118O THR* 4.1 15.3 - - + +
119O ILE* 1.3 79.0 - - - +
121O PRO* 1.3 77.6 - - + +
122O LYS* 3.0 19.1 - - + -
123O ASP* 2.8 29.6 + - - +
124O ILE 3.6 2.3 + - - -
45P ARG* 5.9 0.2 - - - +
47P SER* 3.9 12.8 - - - +
50P ILE* 3.3 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 121 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120O MET* 1.3 86.9 - - + +
122O LYS* 1.3 61.7 + - - +
123O ASP 3.1 0.2 + - - -
124O ILE* 3.4 7.1 + - + +
125O GLN* 3.1 33.7 + - - +
47P SER* 4.2 12.1 - - - +
49P LEU* 3.6 39.0 - - + -
50P ILE* 3.5 11.2 - - + +
53P GLU* 3.5 31.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-237J C 5.3 7.9 + - - -
113K HIS* 3.9 16.8 + - + +
115K LYS* 6.3 1.6 - - - +
116O ARG* 3.8 26.8 - - - +
120O MET* 2.9 21.1 + - + -
121O PRO* 1.3 78.4 - - - +
123O ASP* 1.3 63.1 + - - +
125O GLN* 3.6 17.4 + - - +
126O LEU* 3.3 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K HIS* 2.8 23.1 + - - -
107O THR* 3.6 22.7 - - + +
110O CYS* 3.9 5.6 - - + -
111O ALA* 3.4 15.4 + - - +
116O ARG* 2.7 37.9 + - - -
119O ILE* 3.5 5.0 - - - -
120O MET 2.8 31.2 + - - +
122O LYS* 1.3 76.3 - - - +
124O ILE* 1.3 55.2 + - - +
126O LEU* 2.8 6.6 + - - +
127O ALA* 2.7 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O LEU* 4.4 17.3 - - + -
104O PHE* 4.8 7.2 - - + -
107O THR* 3.5 30.5 - - + +
120O MET 4.4 3.1 - - - +
121O PRO* 3.6 7.6 - - + +
123O ASP* 1.3 76.8 - - - +
125O GLN* 1.3 58.6 + - + +
127O ALA* 3.1 3.3 + - - +
128O ARG* 2.9 37.3 + - + +
50P ILE* 3.8 24.9 - - + -
53P GLU* 4.5 23.8 - - + +
54P THR* 4.6 16.8 - - - +
57P VAL* 4.2 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121O PRO* 3.1 29.8 + - - +
122O LYS* 3.6 16.3 - - - +
124O ILE* 1.3 75.7 - - + +
126O LEU* 1.3 57.8 + - - +
128O ARG* 4.0 5.2 - - - +
129O ARG* 2.8 32.0 + - - +
134O ARG* 5.2 7.7 - - + +
53P GLU* 2.6 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109K LEU* 4.1 34.3 - - + +
110K CYS* 4.6 1.3 - - - -
113K HIS* 3.5 35.4 - - + +
126K LEU* 4.7 8.1 - - + -
110O CYS* 3.3 27.6 - - + -
122O LYS 3.3 11.4 + - - +
123O ASP 2.8 11.2 + - - +
125O GLN* 1.3 73.2 - - - +
127O ALA* 1.3 66.7 + - - +
129O ARG* 3.4 4.2 + - - +
130O ILE* 3.0 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130K ILE* 3.7 9.8 - - - +
103O LEU* 4.3 15.0 - - + -
106O ASP* 4.4 9.6 - - + -
107O THR 4.4 17.0 - - - +
110O CYS* 4.4 11.4 - - - -
123O ASP 2.7 14.7 + - - +
124O ILE* 3.1 12.1 + - - +
126O LEU* 1.3 75.9 - - - +
128O ARG* 1.3 59.4 + - - +
130O ILE* 3.0 1.4 + - - -
131O ARG* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O TYR* 4.0 7.2 + - - -
103O LEU* 4.0 15.7 - - + -
124O ILE* 2.9 24.3 + - + +
125O GLN* 4.0 3.9 - - - +
127O ALA* 1.3 74.2 - - - +
129O ARG* 1.3 66.4 + - - +
131O ARG* 3.3 8.4 + - - +
132O GLY 2.9 17.5 + - - -
133O GLU* 2.9 42.9 + - + +
134O ARG* 3.0 67.1 + - + +
57P VAL* 4.6 26.4 + - - +
60P VAL* 4.4 25.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K ASP* 5.6 4.5 + - - -
109K LEU* 3.5 41.7 - - + +
125O GLN 2.8 25.4 + - - +
126O LEU* 3.6 8.1 - - - +
127O ALA 3.2 0.2 - - - -
128O ARG* 1.3 72.5 - - - +
130O ILE* 1.3 62.1 + - + +
132O GLY* 3.0 20.1 + - - -
134O ARG* 4.1 13.8 - - + +
135O ALA* 2.8 43.4 + - - +
110Q ASN* 5.6 4.6 - - - +
112Q GLN* 4.9 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K ASP* 4.2 31.7 - - + +
109K LEU* 4.7 3.1 - - + -
110K CYS* 3.6 23.1 - - - -
127K ALA* 3.9 22.7 - - - +
130K ILE* 3.5 26.7 - - + -
131K ARG* 3.9 18.6 - - + +
126O LEU* 3.0 42.8 + - + +
129O ARG* 1.3 80.5 - - + +
131O ARG* 1.3 65.4 + - - +
132O GLY* 3.0 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130K ILE* 4.0 21.6 + - + +
131K ARG* 5.2 2.9 - - - +
99O TYR* 3.5 18.4 - - - -
102O ALA* 3.6 9.7 - - - +
103O LEU* 3.3 39.1 - - - +
106O ASP* 2.6 31.1 + - - +
127O ALA 2.9 18.2 + - - +
128O ARG* 3.4 13.0 - - - +
130O ILE* 1.3 75.1 - - - +
132O GLY* 1.3 58.4 + - - +
133O GLU* 2.5 49.6 + - + +
95P ARG* 5.6 3.0 - - - +
99Q ARG* 3.7 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128O ARG 2.9 3.8 + - - -
129O ARG 3.0 11.6 + - - -
130O ILE 3.0 5.5 - - - -
131O ARG* 1.3 78.7 - - - +
133O GLU* 1.3 64.2 + - - +
134O ARG 3.6 6.0 - - - +
135O ALA 5.6 0.4 - - - -
99Q ARG* 4.7 10.8 + - - -
----------------------------------------------------------
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