Contacts of the helix formed by residues 120 - 132 (chain K) 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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232I G 4.3 8.1 - - - +
233I C 3.5 23.1 - - - +
116K ARG* 3.6 35.2 - - - +
118K THR* 4.2 4.5 - - + +
119K ILE* 1.3 80.6 - - - +
121K PRO* 1.3 78.1 - - + +
122K LYS* 3.6 27.1 - - + +
123K ASP* 2.8 29.4 + - - +
124K ILE 3.3 3.5 + - - -
47L SER* 3.7 16.2 - - - +
50L ILE* 3.2 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 121 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120K MET* 1.3 86.5 - - + +
122K LYS* 1.3 63.1 + - - +
124K ILE* 3.1 5.9 + - + +
125K GLN* 2.9 30.5 + - - +
47L SER* 3.9 13.7 - - - +
49L LEU* 3.2 46.2 - - + +
50L ILE* 3.4 8.9 - - + -
53L GLU* 3.6 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233I C 4.5 6.9 + - - -
114K ALA* 6.0 0.2 - - - -
116K ARG* 3.8 22.9 - - - +
120K MET* 3.1 34.4 - - + +
121K PRO* 1.3 79.3 - - - +
123K ASP* 1.3 66.8 + - - +
125K GLN* 3.1 19.6 + - - +
126K LEU* 3.0 19.8 + - - +
113O HIS* 4.1 24.5 + - + +
115O LYS* 5.0 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K THR* 3.6 16.8 - - + +
110K CYS* 3.9 13.5 - - + +
111K ALA* 3.6 12.0 + - - -
116K ARG* 2.5 48.1 + - - -
119K ILE* 3.4 4.7 - - - -
120K MET* 2.8 25.4 + - - +
122K LYS* 1.3 71.5 - - - +
124K ILE* 1.3 69.1 + - - +
126K LEU* 2.7 17.0 + - - +
127K ALA* 3.1 9.7 + - - +
113O HIS* 2.8 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K LEU* 4.0 25.1 - - + -
104K PHE* 4.5 11.2 - - + -
107K THR* 3.4 29.5 - - + +
120K MET 3.3 0.4 + - - -
121K PRO* 3.1 8.4 + - + +
123K ASP* 1.3 75.3 - - - +
125K GLN* 1.3 64.2 + - + +
127K ALA* 3.1 5.2 + - - +
128K ARG* 3.0 36.0 + - - +
50L ILE* 3.8 25.8 - - + -
53L GLU* 4.6 18.4 - - + -
54L THR* 4.1 21.3 - - - +
57L VAL* 4.4 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K PRO* 2.9 18.5 + - - +
122K LYS* 3.2 21.8 - - - +
123K ASP 2.8 1.8 + - - -
124K ILE* 1.3 77.4 - - + +
126K LEU* 1.3 56.4 + - - +
128K ARG* 3.6 6.6 + - - +
129K ARG* 3.0 28.1 + - - +
53L GLU* 2.6 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110K CYS* 3.7 21.5 - - - -
122K LYS 3.0 9.8 + - - +
123K ASP 2.7 14.7 + - - +
125K GLN* 1.3 70.9 - - - +
127K ALA* 1.3 63.9 + - - +
129K ARG* 3.9 6.0 - - + +
130K ILE* 3.0 47.9 + - + +
109O LEU* 4.0 30.3 - - + +
110O CYS* 4.6 9.0 - - - -
113O HIS* 3.6 38.1 - - + +
126O LEU* 4.7 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K LEU* 4.5 11.2 - - + -
106K ASP* 4.3 34.1 - - + +
107K THR 4.5 1.3 - - - +
110K CYS* 4.3 6.4 - - - -
123K ASP 3.1 8.6 + - - +
124K ILE* 3.1 12.5 + - - +
126K LEU* 1.3 77.9 - - - +
128K ARG* 1.3 52.2 + - - +
130K ILE* 3.3 1.6 + - - +
131K ARG* 2.7 42.7 + - - +
130O ILE* 3.9 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K TYR* 3.8 6.9 + - - -
103K LEU* 4.0 15.0 - - + -
124K ILE* 3.0 22.9 + - - +
125K GLN* 4.1 7.2 - - - +
127K ALA* 1.3 73.7 - - - +
129K ARG* 1.3 66.8 + - - +
131K ARG* 3.5 5.8 + - - -
132K GLY 3.0 3.6 + - - -
133K GLU* 2.8 64.1 + - + +
134K ARG* 3.6 32.3 + - - +
57L VAL* 3.6 34.1 - - - +
60L VAL* 4.5 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125K GLN 3.0 18.7 + - - +
126K LEU* 3.9 7.9 - - + +
127K ALA 3.4 0.2 - - - -
128K ARG* 1.3 75.5 - - - +
130K ILE* 1.3 62.9 + - + +
132K GLY* 2.9 20.4 + - - -
133K GLU 4.6 7.4 + - - -
134K ARG* 4.8 22.0 - - - +
106O ASP* 5.6 3.6 - - - +
109O LEU* 4.5 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126K LEU* 3.0 38.9 + - + +
127K ALA 3.8 1.8 - - - +
129K ARG* 1.3 77.5 - - + +
131K ARG* 1.3 57.4 + - - +
132K GLY* 2.9 10.2 + - - -
106O ASP* 4.1 31.0 - - + +
109O LEU* 5.5 1.1 - - + -
110O CYS* 3.6 31.4 - - - -
127O ALA* 3.7 23.1 - - - +
130O ILE* 3.5 29.8 - - + -
131O ARG* 4.0 19.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K TYR* 3.3 22.0 + - - -
102K ALA* 3.2 12.9 - - - +
103K LEU* 3.2 44.1 - - - +
106K ASP* 2.9 29.7 + - - +
127K ALA 2.7 31.1 + - - +
128K ARG 3.8 4.3 - - - +
130K ILE* 1.3 71.1 - - - +
132K GLY* 1.3 61.3 + - - +
133K GLU* 3.0 38.0 + - + +
95L ARG* 5.3 3.4 - - - +
99M ARG* 4.0 16.5 + - - -
130O ILE* 3.9 20.8 + - + +
131O ARG* 5.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129K ARG 2.9 14.4 + - - -
130K ILE 2.9 7.7 - - - -
131K ARG* 1.3 79.8 - - - +
133K GLU* 1.3 63.3 + - - +
134K ARG* 4.2 18.5 + - - -
99M ARG* 4.8 10.2 + - - -
----------------------------------------------------------
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