Contacts of the helix formed by residues 55 - 67 (chain B) in PDB entry 1O69
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 SER 55 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASN* 3.7 27.3 + - - +
53B LEU* 3.2 4.7 - - - +
54B ASN* 1.3 85.6 + - - +
56B ALA* 1.3 63.8 + - - +
57B THR* 3.4 5.7 + - - -
58B ALA* 2.9 26.1 + - - +
59B ALA* 3.1 19.1 + - - +
191B GLY 3.9 0.2 - - - -
192B GLY* 3.7 14.4 - - - +
395B X04 3.5 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 1.3 69.9 - - - +
57B THR* 1.3 58.0 + - - +
59B ALA* 3.1 4.3 + - - +
60B LEU* 2.9 34.1 + - - +
157B ALA* 4.2 2.0 - - + -
177B VAL* 3.5 23.8 - - + -
178B TYR 4.0 1.3 - - - +
179B SER* 3.9 15.0 - - - -
192B GLY* 3.8 5.3 - - - -
395B X04 2.9 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLN* 3.1 19.9 + - - +
227A ASN* 4.4 5.8 - - - +
55B SER* 3.2 5.4 - - - -
56B ALA* 1.3 75.5 - - - +
58B ALA* 1.3 56.5 + - - +
60B LEU* 3.3 3.6 + - - -
61B HIS* 2.8 29.2 + - - +
84B ALA* 3.1 31.3 + - - +
87B ALA* 5.0 0.2 - - + -
88B PRO* 3.6 7.3 - - + +
91B TYR* 3.5 35.4 - - + +
395B X04 2.9 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.3 5.8 - - + -
54B ASN* 3.8 7.0 - - - +
55B SER* 2.9 25.1 + - - +
56B ALA 3.2 0.2 - - - -
57B THR* 1.3 76.4 - - - +
59B ALA* 1.3 57.1 + - - +
61B HIS* 3.3 3.0 + - - +
62B LEU* 2.9 34.3 + - - +
228B TYR* 3.6 47.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.5 24.0 - - + +
55B SER 3.1 8.2 + - - +
56B ALA* 3.1 10.0 + - - +
58B ALA* 1.3 80.3 - - - +
60B LEU* 1.3 57.2 + - - +
62B LEU* 3.4 2.3 + - - +
63B ALA* 2.8 29.6 + - - +
177B VAL* 3.6 27.1 - - + -
193B MET 4.1 6.5 - - - +
194B LEU* 3.7 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA 2.9 14.0 + - - +
57B THR 3.7 5.8 - - - +
59B ALA* 1.3 72.7 - - - +
61B HIS* 1.3 65.8 + - - +
63B ALA* 3.3 3.4 + - - +
64B LEU* 2.9 28.8 + - - +
84B ALA 4.2 3.6 - - - +
85B SER* 3.6 27.1 - - - +
88B PRO* 4.1 11.0 - - + -
127B ILE* 4.2 21.1 - - + -
153B ILE* 3.6 28.5 - - + -
155B ASP* 4.2 14.4 - - + +
177B VAL* 3.7 16.2 - - + -
395B X04 3.5 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 6.0 1.6 - + - -
57B THR 2.8 20.6 + - - +
58B ALA* 3.3 8.9 + - - +
60B LEU* 1.3 74.0 - - - +
62B LEU* 1.3 64.0 + - - +
64B LEU* 3.3 2.5 + - - +
65B ARG* 3.0 20.3 + - + +
88B PRO* 3.7 15.4 - - + +
91B TYR* 3.6 33.5 - + + +
92B LEU* 3.9 26.2 - - + +
226B TYR* 3.5 36.5 + + - -
228B TYR* 2.7 30.1 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.8 25.6 - - + -
58B ALA 2.9 17.4 + - - +
59B ALA 3.8 3.6 - - - +
60B LEU 3.3 0.2 - - - -
61B HIS* 1.3 75.2 - - - +
63B ALA* 1.3 66.9 + - - +
65B ARG* 3.9 4.2 - - + +
66B VAL* 2.8 31.0 + - + +
194B LEU* 4.3 3.6 - - + -
205B ALA* 3.5 35.4 - - + +
208B TYR* 3.8 15.5 - - + -
209B SER* 3.9 15.9 - - - -
226B TYR* 3.6 38.1 - - + -
228B TYR* 3.8 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ALA 2.8 21.1 + - - +
60B LEU* 3.3 5.8 + - - +
62B LEU* 1.3 72.7 - - - +
64B LEU* 1.3 57.8 + - - +
66B VAL 3.8 0.3 - - - -
67B ALA* 2.8 30.8 + - - +
153B ILE* 3.9 19.1 - - + -
175B PHE* 3.8 43.4 - - + -
194B LEU* 4.0 7.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU 2.9 16.2 + - - +
61B HIS 3.7 1.8 - - - +
63B ALA* 1.3 76.9 - - - +
65B ARG* 1.3 63.9 + - - +
67B ALA* 3.2 9.3 + - - +
68B GLY 3.3 0.2 + - - -
69B VAL* 3.2 37.4 + - + +
75B VAL* 4.0 18.4 - - + -
88B PRO* 3.8 32.3 - - + +
89B ILE* 3.8 20.2 - - + +
92B LEU* 3.7 15.9 - - + -
125B ALA* 4.2 2.2 - - + -
127B ILE* 4.0 24.0 - - + -
153B ILE* 3.5 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B HIS* 3.0 17.6 + - + +
62B LEU* 3.9 7.2 - - + +
64B LEU* 1.3 76.4 - - - +
66B VAL* 1.3 59.3 + - - +
68B GLY* 2.9 21.3 + - - -
69B VAL 4.1 6.1 + - - +
70B LYS* 4.8 11.4 + - - +
92B LEU* 3.9 21.2 - - + +
208B TYR* 3.4 29.4 + - + +
223B ASP* 2.8 40.6 + - - -
224B TYR* 3.1 42.2 + - - -
226B TYR* 2.8 36.1 + - - +
----------------------------------------------------------
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 LEU 2.8 20.3 + - - +
63B ALA 4.2 1.3 - - - +
65B ARG* 1.3 76.7 - - - +
67B ALA* 1.3 61.4 + - - +
68B GLY* 3.1 1.8 + - - -
175B PHE* 4.1 9.2 - - + -
201B LYS* 3.6 51.3 - - + +
204B LYS* 4.1 11.4 - - + -
205B ALA* 3.8 31.6 - - + +
208B TYR* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA 2.8 19.4 + - - +
64B LEU* 3.6 8.7 - - - +
65B ARG 3.2 0.2 - - - -
66B VAL* 1.3 76.8 - - - +
68B GLY* 1.3 58.9 + - - +
69B VAL* 3.5 8.1 + - + +
124B LYS* 4.9 8.2 - - - +
125B ALA* 5.0 0.7 - - + -
151B VAL* 4.0 38.7 - - + +
153B ILE* 4.6 5.2 - - + -
175B PHE* 4.3 7.3 - - + -
201B LYS* 5.3 4.0 - - - +
----------------------------------------------------------
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