Contacts of the helix formed by residues 65 - 77 (chain B) in PDB entry 1IAO
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 PRO 65 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASN 5.4 0.9 - - - +
63B SER 2.7 22.1 - - - +
64B GLN* 1.3 79.4 - - - +
66B GLU* 1.3 70.4 + - - +
68B LEU* 4.7 3.1 - - + +
69B ASP* 2.7 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLN* 2.6 37.0 - - - +
65B PRO* 1.3 89.0 - - - +
67B ILE* 1.3 74.8 + - + +
69B ASP* 3.9 1.5 - - - +
70B ARG* 3.0 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 4.3 9.0 - - + +
60B TYR* 4.9 4.5 - - + +
61B TRP* 3.6 43.3 - - + +
64B GLN* 2.7 34.6 + - + +
66B GLU* 1.3 80.3 - - + +
68B LEU* 1.3 67.0 + - - +
70B ARG* 3.0 5.9 + - - +
71B THR* 3.0 29.3 + - - +
330B ALA* 4.1 20.4 - - + -
331B HIS* 4.7 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 4.4 2.5 - - + -
45B GLY 4.0 10.1 - - - +
46B GLU* 4.3 7.0 - - + +
47B TYR* 4.3 14.6 - - + -
61B TRP 3.5 14.5 + - - +
62B ASN* 3.3 43.7 - - + +
64B GLN 2.9 10.1 + - - +
65B PRO* 4.5 1.8 - - + +
67B ILE* 1.3 77.6 - - - +
69B ASP* 1.3 66.3 + - - +
71B THR* 4.0 0.7 - - - -
72B ARG* 2.9 67.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PRO* 2.7 34.3 + - - +
66B GLU* 4.2 1.6 - - - +
68B LEU* 1.3 89.1 - - - +
70B ARG* 1.3 63.3 + - - +
71B THR 3.3 0.2 - - - -
72B ARG* 3.9 18.7 + - - +
73B ALA* 3.5 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN* 4.5 2.4 + - - -
66B GLU 3.0 20.6 + - - +
67B ILE* 3.0 5.4 + - - +
69B ASP* 1.3 75.3 - - - +
71B THR* 1.3 68.2 + - - +
73B ALA* 3.6 4.9 + - - +
74B GLU* 3.2 30.5 + - - +
77B THR* 4.8 0.9 + - - -
328B HIS* 2.8 58.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.6 8.5 - - + +
28B THR* 4.8 5.2 - - + -
40B TYR* 3.5 37.9 - - + -
47B TYR* 2.7 31.3 + - + +
67B ILE* 3.0 17.7 + - - +
68B LEU 4.0 3.8 - - - -
70B ARG* 1.3 76.8 - - - +
72B ARG* 1.3 67.2 + - - +
74B GLU* 2.9 36.8 + - - +
328B HIS 5.5 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.9 1.0 - - - +
40B TYR* 3.5 22.4 + - - +
45B GLY* 3.0 25.5 + - - +
46B GLU* 4.6 7.3 + - - +
68B LEU* 2.9 48.9 + - + +
69B ASP* 3.9 17.3 + - - +
70B ARG 3.4 0.2 - - - -
71B THR* 1.3 80.8 - - - +
73B ALA* 1.3 60.6 + - - +
75B VAL* 3.2 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP 3.5 14.0 + - - +
70B ARG* 3.9 4.0 - - - +
71B THR 3.3 0.8 - - - -
72B ARG* 1.3 75.4 - - - +
74B GLU* 1.3 51.4 + - - +
75B VAL* 3.0 8.5 - - - -
76B ASP* 2.9 12.6 + - + +
77B THR* 2.6 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.8 7.7 - - + +
28B THR* 4.7 1.2 - - - +
70B ARG* 3.2 23.6 + - - +
71B THR* 2.9 34.9 + - - +
73B ALA* 1.3 77.5 - - - +
75B VAL* 1.3 56.9 + - - +
76B ASP 3.1 0.2 - - - -
77B THR* 3.0 11.2 - - - +
78B ALA* 3.1 32.6 + - + +
79B CYS* 3.6 4.0 + - - -
326B ALA 4.8 1.8 - - - +
327B VAL* 3.1 33.5 - - + +
328B HIS* 3.2 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.4 35.6 - - + +
26B LEU* 3.8 20.2 - - + +
42B SER* 4.1 14.8 - - - +
72B ARG 3.2 19.6 + - - +
73B ALA* 4.4 1.8 - - - -
74B GLU* 1.3 79.0 - - - +
76B ASP* 1.3 72.7 + - + +
79B CYS* 3.0 11.8 - - + +
80B ARG* 2.9 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA* 2.9 11.2 + - + +
75B VAL* 1.3 91.9 - - + +
77B THR* 1.3 65.9 + - + +
80B ARG* 3.1 40.0 + - - +
81B HIS* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG 4.8 1.0 + - - -
73B ALA* 2.6 28.9 + - + +
74B GLU* 3.0 17.4 - - - +
76B ASP* 1.3 77.0 - - + +
78B ALA* 1.3 55.8 + - - +
81B HIS* 2.9 24.0 - - - +
325B GLN* 3.7 18.5 - - - +
----------------------------------------------------------
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