Contacts of the helix formed by residues 41 - 52 (chain A) 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 41 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 1.3 72.2 - - - +
42A TRP* 1.3 64.7 + - - +
44A ALA* 3.1 11.8 + - - +
45A ALA 3.3 9.0 + - - -
66A LEU* 4.0 12.5 - - - +
76A ILE* 3.5 14.1 + - - +
77A PRO 3.3 25.1 - - - -
78A HIS* 2.9 17.1 + - - -
80A VAL 5.7 0.2 - - - +
115A GLN* 3.8 10.3 + - - +
119A HIS* 2.9 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 1.3 80.2 + - - +
43A ALA* 1.3 70.4 + - - +
45A ALA* 3.2 10.6 + - - +
46A PHE* 3.1 40.7 + + - -
115A GLN* 3.1 33.5 + - - +
116A PRO* 3.8 38.8 - - + +
118A VAL* 3.5 24.5 - - + -
119A HIS* 4.4 1.1 - - - -
179A SER 4.4 6.1 - - - -
180A GLY* 3.6 31.5 + - - -
181A MET* 5.2 2.9 - - + -
254A PHE* 5.0 5.4 - + - -
258A ILE* 4.4 13.0 - - + -
376A TRP* 4.7 12.8 - + - -
383A VAL* 5.4 4.0 - - + -
384A LEU* 5.0 10.3 - - + -
387A LEU* 4.9 6.3 - - + -
436A TRP* 3.4 24.9 - + - -
504A GOL 3.0 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 4.2 19.7 - - + -
40A TRP* 3.6 23.7 - - + +
41A SER 3.2 0.4 - - - -
42A TRP* 1.3 84.4 - - - +
44A ALA* 1.3 56.7 + - - +
46A PHE* 3.1 2.9 + - - +
47A VAL* 2.8 36.0 + - + +
436A TRP* 3.7 28.9 - - + +
504A GOL 4.6 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR 6.1 0.7 - - - +
39A MET* 3.9 30.5 - - + -
40A TRP 2.7 21.8 + - - +
41A SER 3.1 5.3 + - - +
43A ALA* 1.3 73.6 - - - +
45A ALA* 1.3 57.7 + - - +
47A VAL* 3.7 9.0 - - - +
48A ALA* 2.9 28.8 + - - +
62A GLU* 3.8 11.2 - - + +
63A LEU* 4.2 3.4 - - + +
66A LEU* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER 3.3 3.4 + - - -
42A TRP 3.2 2.6 + - - +
43A ALA 3.2 0.6 - - - -
44A ALA* 1.3 77.7 - - - +
46A PHE* 1.3 61.8 + - + +
48A ALA 3.2 2.1 + - - -
49A ILE* 3.1 20.8 + - + +
63A LEU* 4.3 6.8 - - - +
118A VAL* 3.3 36.3 - - + +
119A HIS* 4.0 26.9 - - + -
122A ALA* 3.3 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TRP* 3.1 46.1 + + - -
43A ALA 3.1 6.0 + - - +
45A ALA* 1.3 73.2 - - - +
47A VAL* 1.3 65.4 + - - +
49A ILE* 3.1 17.1 + - + +
50A GLY 3.0 17.2 + - - -
118A VAL* 4.0 24.5 - - + -
121A ILE* 6.2 0.7 - - + -
383A VAL* 3.5 28.0 - - + -
386A TRP* 3.7 37.2 - + + -
387A LEU* 4.6 13.7 - - + -
436A TRP* 3.6 32.8 - + + +
439A ALA* 3.1 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.2 9.3 - - + +
29A THR* 3.7 37.5 - - + +
30A THR 5.1 1.6 - - - +
31A ALA* 5.8 0.9 - - - -
43A ALA* 2.8 29.9 + - + +
44A ALA* 3.7 8.1 - - - +
46A PHE* 1.3 72.8 - - - +
48A ALA* 1.3 58.4 + - - +
50A GLY* 3.1 2.6 + - - -
51A LEU* 2.9 43.3 + - + +
62A GLU* 4.1 6.1 - - + +
435A SER* 3.8 31.9 - - - -
436A TRP 4.8 1.3 - - - +
439A ALA* 4.3 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 2.9 15.7 + - - +
45A ALA 3.2 8.7 + - - +
47A VAL* 1.3 75.0 - - - +
49A ILE* 1.3 62.4 + - - +
51A LEU* 3.3 6.0 + - - -
52A ALA* 3.0 22.0 + - - +
59A ALA* 3.5 32.2 - - - +
62A GLU* 4.5 3.3 - - + +
63A LEU* 3.9 18.8 - - + -
122A ALA* 4.2 3.1 - - + -
126A ILE* 4.2 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA* 3.1 17.1 + - + +
46A PHE* 3.1 22.2 + - + +
48A ALA* 1.3 76.4 - - - +
50A GLY* 1.3 63.1 + - - +
52A ALA* 3.5 7.2 + - - +
53A PRO* 3.2 17.8 - - - +
118A VAL* 5.5 0.9 - - + +
121A ILE* 4.3 5.4 - - + -
122A ALA* 3.6 30.3 - - + +
125A ARG* 4.1 14.6 - - + -
129A HIS* 5.0 0.7 + - - -
386A TRP* 3.8 33.7 - - + -
439A ALA 5.0 2.2 - - - +
443A ASP* 3.5 39.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.8 8.7 - - - -
46A PHE 3.0 11.1 + - - -
47A VAL 3.1 3.3 + - - -
49A ILE* 1.3 78.9 - - - +
51A LEU* 1.3 59.6 + - - +
53A PRO* 3.3 15.1 - - - +
54A LEU* 3.7 4.3 - - - +
439A ALA* 3.7 32.0 - - - +
442A LEU* 3.7 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.0 24.5 - - + +
21A ARG* 5.7 1.6 - - - +
24A ASP* 6.1 0.2 - - - +
29A THR* 4.5 4.0 - - - +
47A VAL* 2.9 37.9 + - + +
48A ALA 3.8 4.0 - - - +
49A ILE 3.3 0.2 - - - -
50A GLY* 1.3 76.3 - - - +
52A ALA* 1.3 59.7 + - - +
53A PRO 3.3 0.2 - - - -
54A LEU* 2.8 32.5 + - + +
55A SER* 2.8 18.1 + - - +
58A ARG* 3.9 46.4 - - + +
59A ALA* 3.8 15.5 - - + +
62A GLU* 4.1 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA 3.0 17.2 + - - +
49A ILE* 3.7 6.3 - - - +
51A LEU* 1.3 76.4 - - - +
53A PRO* 1.3 68.9 - - + +
54A LEU 3.3 0.5 + - - -
55A SER 3.9 6.6 + - - -
56A VAL* 3.9 19.4 + - + +
59A ALA* 4.0 8.1 - - + -
125A ARG 4.4 0.9 - - - +
126A ILE* 4.1 23.8 - - + +
129A HIS* 3.6 27.2 + - + +
133A ARG* 6.2 0.3 - - - +
----------------------------------------------------------
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