Contacts of the helix formed by residues 55 - 69 (chain B) in PDB entry 5OIV
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
----------------------------------------------------------
51B LEU* 2.8 19.2 + - - +
52B ALA 3.8 0.6 + - - -
53B PRO 3.8 0.8 - - - -
54B LEU* 1.3 80.2 - - - +
56B VAL* 1.3 64.1 + - - +
57B GLU* 3.5 9.2 + - - +
58B ARG* 3.0 29.9 + - - +
59B ALA* 2.9 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ALA* 3.9 16.5 + - - +
55B SER* 1.3 71.9 - - - +
57B GLU* 1.3 64.6 + - + +
59B ALA* 3.2 7.0 + - - +
60B VAL* 3.0 23.6 + - + +
126B ILE* 4.0 21.3 - - + +
129B HIS* 4.3 5.8 - - + -
130B ALA* 4.2 21.3 - - + +
133B ARG* 5.1 4.5 - - + -
137B THR* 3.6 38.6 - - + +
140B VAL* 4.1 17.5 - - + -
141B ALA* 4.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 3.1 7.7 + - - +
56B VAL* 1.3 78.4 - - + +
58B ARG* 1.3 57.5 + - - +
60B VAL* 3.3 5.4 + - - +
61B VAL* 3.1 31.1 + - + +
140B VAL* 3.8 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 6.5 0.7 - - - -
24B ASP* 2.7 43.4 + - - +
26B GLY 3.5 13.0 + - - -
27B THR* 3.5 3.1 + - - -
28B MET 3.4 15.2 - - - +
29B THR* 3.4 7.3 + - - -
51B LEU* 3.8 20.9 - - + +
55B SER* 3.0 25.2 + - - +
57B GLU* 1.3 73.0 - - - +
59B ALA* 1.3 66.5 + - - +
61B VAL* 3.3 16.8 + - - +
62B GLU* 2.8 47.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
48B ALA* 3.5 32.0 - - - +
51B LEU* 3.8 12.0 - - + +
52B ALA* 3.8 14.8 - - - +
55B SER 2.9 17.3 + - - +
56B VAL* 3.2 5.8 + - - +
58B ARG* 1.3 76.0 - - - +
60B VAL* 1.3 60.6 + - - +
62B GLU* 3.2 13.2 + - - +
63B LEU* 3.5 10.2 + - - +
126B ILE* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 3.0 19.6 + - + +
57B GLU* 3.6 7.2 - - - +
59B ALA* 1.3 73.8 - - - +
61B VAL* 1.3 63.3 + - + +
63B LEU* 3.2 5.4 + - - +
64B ASP* 2.8 29.9 + - - +
126B ILE* 4.1 25.8 - - + -
140B VAL* 4.5 16.8 - - + -
141B ALA* 4.6 2.7 - - - -
144B PHE* 3.6 28.7 - - + -
147B ARG* 3.3 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY 4.9 0.7 - - - +
27B THR* 3.9 30.5 - - + +
57B GLU* 3.1 21.0 + - + +
58B ARG* 3.3 30.3 + - - +
60B VAL* 1.3 77.1 - - + +
62B GLU* 1.3 57.4 + - - +
64B ASP* 3.5 10.4 - - + +
65B THR* 2.8 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR 4.4 2.0 - - - -
28B MET* 3.8 1.2 - - - -
29B THR* 3.0 46.0 + - - +
39B MET* 3.1 27.6 - - + +
44B ALA* 3.9 25.7 - - + +
47B VAL* 3.9 10.4 - - + +
48B ALA* 4.4 4.3 - - + -
51B LEU* 4.1 7.6 - - + +
58B ARG* 2.8 43.1 + - - +
59B ALA 3.5 9.6 - - - +
60B VAL 3.2 0.6 - - - -
61B VAL* 1.3 78.7 - - - +
63B LEU* 1.3 61.7 + - - +
65B THR* 3.5 0.3 + - - -
66B LEU* 3.2 18.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
44B ALA 4.2 12.8 - - - +
45B ALA* 4.3 11.2 - - - +
48B ALA* 3.9 15.3 - - + -
59B ALA 3.5 8.2 + - - +
60B VAL 3.2 3.0 + - - +
62B GLU* 1.3 74.1 - - - +
64B ASP* 1.3 62.1 + - - +
66B LEU* 3.7 7.2 - - + +
67B LEU* 2.9 38.3 + - + +
119B HIS* 4.7 14.6 - - + +
122B ALA* 4.3 9.2 - - + -
123B VAL* 3.9 26.0 - - + -
126B ILE* 3.6 26.7 - - + -
144B PHE* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 2.8 22.6 + - - +
61B VAL* 3.5 11.4 - - + +
63B LEU* 1.3 77.8 - - - +
65B THR* 1.3 56.7 + - - +
67B LEU 3.4 0.5 + - - -
68B SER* 2.9 26.6 + - - -
144B PHE* 3.7 2.5 - - - -
147B ARG* 2.7 40.6 + - - -
148B ARG* 2.8 50.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR* 2.7 40.4 + - - +
28B MET* 4.1 19.7 - - + -
39B MET* 4.2 4.8 - - + +
61B VAL* 2.8 13.3 + - - +
62B GLU 3.7 3.6 - - - -
64B ASP* 1.3 77.2 - - - +
66B LEU* 1.3 63.3 + - - +
68B SER* 2.6 25.3 + - - +
69B ALA* 3.6 5.7 + - - +
80B VAL* 5.2 1.0 - - + +
108B ARG* 3.6 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B MET* 3.8 18.7 - - + -
41B SER* 3.9 23.3 - - - +
44B ALA* 4.3 6.7 - - + -
62B GLU 3.2 12.9 + - - +
63B LEU* 3.7 12.8 - - + +
65B THR* 1.3 79.4 - - - +
67B LEU* 1.3 66.2 + - + +
69B ALA* 3.0 19.8 + - - +
70B GLN* 3.6 3.5 + - - -
76B ILE* 3.8 27.4 - - + +
77B PRO* 4.5 1.3 - - + +
80B VAL* 3.9 21.8 - - + -
119B HIS* 3.4 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 2.9 26.6 + - + +
66B LEU* 1.3 69.8 - - + +
68B SER* 1.3 61.4 + - - +
69B ALA 3.0 5.2 - - - -
70B GLN* 3.0 37.2 + - - +
76B ILE* 3.8 29.2 - - + -
119B HIS* 6.4 0.4 - - + -
144B PHE* 4.3 11.4 - - + -
148B ARG* 3.7 53.5 + - + +
151B ASP* 4.3 10.7 - - + +
152B LEU* 4.4 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASP 2.9 15.6 + - - -
65B THR* 2.6 23.4 + - - +
67B LEU* 1.3 76.9 - - - +
69B ALA* 1.3 56.4 + - - +
70B GLN 3.4 1.6 + - - +
105B PRO* 4.3 8.8 - - - +
108B ARG* 4.2 20.9 + - - +
148B ARG* 4.2 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B THR 4.2 2.2 - - - +
66B LEU 3.0 12.6 + - - +
67B LEU 3.0 0.8 - - - -
68B SER* 1.3 77.3 + - - +
70B GLN* 1.3 64.8 + - - +
71B TRP* 3.4 3.1 + - - -
77B PRO* 3.5 14.6 - - + +
80B VAL* 3.5 35.9 - - + -
105B PRO* 3.5 18.7 - - - +
108B ARG* 4.1 8.5 - - + -
110B THR* 3.9 12.1 - - + -
----------------------------------------------------------
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