Contacts of the helix formed by residues 87 - 99 (chain V) in PDB entry 6L49
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 THR 87 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-132J G 3.4 24.5 - - - +
44U GLY* 4.4 2.5 - - - -
47U ALA* 3.8 4.7 - - - +
83V ARG* 4.2 11.3 + - - +
85V THR* 3.4 18.4 + - + -
86V ILE* 1.3 76.8 - - - +
88V SER* 1.3 65.9 + - - +
89V ARG* 3.2 15.5 + - - +
90V GLU* 2.6 30.0 + - - +
91V ILE* 3.5 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46U GLY* 3.3 27.2 + - - +
47U ALA* 4.6 3.5 - - - +
50U TYR* 4.3 8.1 - - - -
87V THR* 1.3 74.3 - - - +
89V ARG* 1.3 60.1 + - - +
90V GLU 3.2 0.2 - - - -
91V ILE* 3.5 9.2 + - - +
92V GLN* 2.9 31.8 + - - +
115V VAL* 3.4 32.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74T GLU 2.7 29.5 + - - -
75T HIS* 2.7 45.1 + - + +
77T LYS* 3.6 33.9 - - - +
83V ARG* 6.3 1.0 - - - +
87V THR* 3.2 12.5 + - - +
88V SER* 1.3 78.4 - - - +
90V GLU* 1.3 58.1 + - - +
92V GLN* 3.4 18.8 + - - +
93V THR* 2.9 31.1 + - - +
96V ARG* 6.1 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75T HIS* 2.8 36.2 + - + -
74V ALA* 3.4 15.6 - - + +
77V LEU* 5.4 0.2 - - - -
78V ALA* 3.9 21.4 - - + +
83V ARG* 2.4 33.0 + - - -
85V THR 3.5 2.9 - - - -
86V ILE* 3.7 20.4 - - + -
87V THR* 2.6 41.9 + - - +
88V SER 3.2 0.2 - - - -
89V ARG* 1.3 74.9 - - - +
91V ILE* 1.3 59.8 + - - +
93V THR* 3.3 10.5 - - - +
94V ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34U LEU* 5.2 4.9 - - + -
47U ALA* 3.7 24.5 - - + -
50U TYR* 3.5 24.2 - - + -
51U LEU* 3.7 35.4 - - + +
70V ILE* 3.8 17.5 - - + +
71V ALA* 5.2 2.5 - - - -
74V ALA* 3.7 20.4 - - + -
86V ILE* 3.7 16.8 - - + -
87V THR 3.5 14.1 - - - +
88V SER* 3.5 3.1 + - - +
90V GLU* 1.3 74.7 - - - +
92V GLN* 1.3 57.2 + - - +
94V ALA* 3.5 1.7 - - - +
95V VAL* 2.9 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50U TYR* 3.3 27.1 + - + +
88V SER* 2.9 20.7 + - - +
89V ARG* 3.4 18.9 + - - +
91V ILE* 1.3 76.5 - - - +
93V THR* 1.3 58.8 + - - +
95V VAL* 3.2 4.9 + - - +
96V ARG* 2.9 43.2 + - - +
108V VAL* 4.0 17.5 - - + +
112V THR* 4.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 93 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71T THR* 3.1 29.5 + - - +
75T HIS* 3.5 28.4 - - + +
77V LEU* 3.7 18.7 - - + +
89V ARG* 2.9 21.1 + - - +
90V GLU 3.3 10.3 - - - +
92V GLN* 1.3 74.7 - - - +
94V ALA* 1.3 60.2 + - - +
96V ARG* 3.5 22.5 + - - +
97V LEU* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 94 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70V ILE* 3.6 18.4 - - + +
73V GLU* 3.9 7.1 - - + +
74V ALA* 3.6 27.8 - - + +
77V LEU* 3.7 7.9 - - + -
90V GLU 2.9 19.6 + - - +
91V ILE 3.5 5.2 - - - +
93V THR* 1.3 76.5 - - - +
95V VAL* 1.3 59.8 + - - +
97V LEU* 3.7 3.5 - - - +
98V LEU* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50U TYR* 3.6 25.4 - - + +
54U VAL* 3.8 21.8 - - + -
70V ILE* 3.8 18.4 - - + -
91V ILE* 2.9 19.8 + - + +
92V GLN 3.2 4.5 + - - +
94V ALA* 1.3 77.0 - - - +
96V ARG* 1.3 58.3 + - - +
98V LEU* 5.1 0.2 - - - -
99V LEU* 3.0 39.3 + - + +
104V ALA* 3.4 24.4 - - - +
107V ALA* 3.7 17.3 - - + -
108V VAL* 4.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 96 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67T ARG* 5.8 3.8 - - - -
68T ASP* 5.1 2.1 - - - +
71T THR* 3.4 36.3 + - + +
74T GLU* 2.6 40.7 + - - +
75T HIS* 4.8 3.8 - - - +
89V ARG* 6.1 2.4 - - - +
92V GLN* 2.9 30.2 + - - +
93V THR* 3.5 26.0 + - - +
95V VAL* 1.3 75.7 - - - +
97V LEU* 1.3 61.6 + - - +
99V LEU 3.9 7.3 - - - +
104V ALA* 4.0 13.4 - - + +
105V LYS* 6.1 0.7 - - - -
108V VAL* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68T ASP* 3.6 50.6 - - + +
71T THR* 3.8 13.5 - - + -
72T TYR* 3.6 27.8 - - + +
92T ARG* 2.8 33.1 + - + +
73V GLU* 3.5 25.6 - - - +
77V LEU* 3.7 26.7 - - + -
93V THR* 2.9 14.3 + - - +
94V ALA 3.7 4.3 - - - +
96V ARG* 1.3 80.3 - - - +
98V LEU* 1.3 60.4 + - - +
99V LEU 4.1 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92T ARG* 2.7 29.9 + - + +
96U LEU* 4.2 18.7 - - + +
66V ILE* 5.7 1.6 - - + -
69V ARG* 3.9 44.4 - - + +
70V ILE* 3.7 31.0 - - + +
73V GLU* 5.0 16.4 - - + +
94V ALA 2.9 19.6 + - - +
95V VAL 4.6 0.2 - - - +
97V LEU* 1.3 71.7 - - - +
99V LEU* 1.3 68.1 + - + +
100V PRO* 3.8 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92T ARG* 5.1 0.2 - - - -
54U VAL* 4.1 13.0 - - + -
58U LEU* 3.9 18.4 - - + -
96U LEU* 3.8 38.4 - - + -
66V ILE* 5.8 0.2 - - + -
70V ILE* 4.9 5.6 - - + -
95V VAL* 3.0 26.9 + - + +
96V ARG 3.9 8.0 - - - +
97V LEU 4.1 1.7 - - - +
98V LEU* 1.3 82.5 - - + +
100V PRO* 1.3 69.3 - - + +
101V GLY 3.9 0.5 + - - -
103V LEU* 3.8 15.9 - - + +
104V ALA* 3.4 20.1 - - + +
107V ALA* 3.8 28.5 - - + -
----------------------------------------------------------
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