Contacts of the helix formed by residues 60 - 73 (chain B) in PDB entry 3IIV
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 LYS 60 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL 5.0 3.2 + - - -
57B GLU 4.9 8.7 + - - +
58B LYS 3.5 20.0 + - - -
61B THR* 1.3 64.7 + - - +
62B MET* 3.3 2.5 - - - +
63B LEU* 3.2 26.7 + - - +
64B GLU* 2.8 55.3 + - + +
95B ARG* 5.0 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASP* 5.9 2.0 - - - -
15B GLY* 5.6 11.7 - - - +
57B GLU 4.8 2.1 + - - -
58B LYS* 3.4 24.8 + - + +
60B LYS* 1.3 74.3 - - - +
62B MET* 1.3 61.9 + - - +
64B GLU* 3.3 17.1 + - - +
65B LEU* 2.9 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.2 11.7 - - + -
49B PHE* 4.5 12.1 - - + +
51B ASP* 3.6 45.3 - - + +
58B LYS 3.5 10.3 + - - +
60B LYS 3.3 1.3 - - - +
61B THR* 1.3 78.2 - - - +
63B LEU* 1.3 65.0 + - + +
65B LEU* 3.1 24.7 + - + +
66B VAL* 2.9 47.9 + - + +
79B VAL* 4.3 18.2 - - + -
80B GLY* 4.6 3.8 - - - +
92B LEU* 4.5 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 3.2 26.3 + - + +
62B MET* 1.3 79.5 - - + +
64B GLU* 1.3 62.6 + - - +
66B VAL* 3.2 5.6 + - - -
67B GLU 3.1 17.2 + - - -
88B THR 5.3 0.4 - - - +
91B GLU* 3.5 37.9 - - + +
92B LEU* 3.6 30.7 - - + -
95B ARG* 3.5 51.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 2.8 58.7 + - + +
61B THR* 3.6 15.8 + - - +
62B MET 3.3 0.2 - - - -
63B LEU* 1.3 71.6 - - - +
65B LEU* 1.3 60.6 + - - +
67B GLU* 3.5 10.7 + - - +
68B LYS* 3.2 21.3 + - - +
95B ARG* 4.2 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.5 32.3 - - + -
15B GLY* 5.1 11.4 - - - +
32B PRO* 4.1 18.6 - - + -
33B VAL* 3.5 31.9 - - + -
49B PHE* 5.6 1.1 - - + -
61B THR* 2.9 14.8 + - + +
62B MET* 3.1 19.5 + - + +
64B GLU* 1.3 75.6 - - - +
66B VAL* 1.3 61.3 + - - +
68B LYS* 3.1 9.8 + - + +
69B VAL* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B MET* 2.9 34.6 + - + +
63B LEU* 3.2 3.5 + - - +
65B LEU* 1.3 76.6 - - - +
67B GLU* 1.3 56.6 + - - +
69B VAL* 3.7 8.7 - - + +
70B ALA* 2.8 32.7 + - - +
77B ILE* 5.7 1.9 - - + +
79B VAL* 4.2 12.6 - - + -
92B LEU* 3.7 36.6 - - + +
95B ARG* 3.6 22.4 - - + -
97B ALA* 3.8 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU 3.1 6.6 + - - +
64B GLU* 3.5 14.5 - - - +
66B VAL* 1.3 75.1 - - - +
68B LYS* 1.3 56.5 + - - +
70B ALA* 3.5 2.3 + - - +
71B GLU* 3.0 43.9 + - - +
95B ARG* 2.7 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASP* 5.1 6.1 + - - -
33B VAL* 3.8 26.8 - - + +
64B GLU 3.2 9.8 + - - +
65B LEU* 3.1 14.4 + - + +
67B GLU* 1.3 74.7 - - - +
69B VAL* 1.3 65.8 + - - +
71B GLU* 3.3 13.4 + - - +
72B GLN* 3.1 54.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 3.9 22.2 - - + +
49B PHE* 3.5 46.0 - - + -
65B LEU* 2.9 27.8 + - + +
66B VAL* 3.7 7.2 - - - +
68B LYS* 1.3 77.0 - - - +
70B ALA* 1.3 58.7 + - - +
72B GLN 3.2 0.7 + - - -
73B ILE* 2.9 48.9 + - + +
77B ILE* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL 2.8 20.6 + - - +
67B GLU 3.7 4.3 - - - +
69B VAL* 1.3 75.7 - - - +
71B GLU* 1.3 61.7 + - + +
72B GLN 3.6 0.2 + - - -
73B ILE 3.9 13.9 + - - +
74B ASP* 4.7 4.0 - - - +
77B ILE* 5.1 5.4 - - + -
95B ARG 4.1 2.9 - - - +
96B GLY* 3.6 36.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 3.0 34.4 + - - +
68B LYS* 3.5 15.3 - - - +
69B VAL 3.2 0.6 - - - -
70B ALA* 1.3 77.3 - - + +
72B GLN* 1.3 67.7 + - + +
74B ASP* 4.7 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 3.2 24.8 - - + +
37B LYS* 3.1 38.5 + - + +
68B LYS* 3.1 50.1 + - - +
69B VAL 4.3 1.1 - - - +
71B GLU* 1.3 87.0 + - + +
73B ILE* 1.3 62.9 + - + +
74B ASP* 4.0 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 4.1 7.0 - - - +
36B GLY* 3.7 10.5 - - - -
37B LYS* 3.6 36.1 - - + +
40B SER* 3.8 11.0 - - - -
47B LEU* 3.7 15.7 - - + -
49B PHE* 4.1 3.8 - - + -
69B VAL* 2.9 42.7 + - + +
70B ALA* 3.9 8.7 - - - +
71B GLU 3.7 0.4 - - - -
72B GLN* 1.3 83.5 - - + +
74B ASP* 1.3 63.6 - - - +
75B ILE* 3.5 33.0 + - + +
77B ILE* 3.8 11.5 - - + +
----------------------------------------------------------
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