Contacts of the helix formed by residues 50 - 66 (chain A) in PDB entry 6CV8
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 50 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU 5.8 0.7 - - - -
39A LEU* 5.2 1.6 - - - -
44A ASP* 4.5 7.6 + - - -
47A SER* 3.2 22.0 + - - -
49A GLY* 1.3 80.7 + - - +
51A TRP* 1.3 60.9 + - - +
52A ASP 3.1 2.5 - - - -
53A PRO* 3.1 20.5 - - - +
54A ILE* 2.9 39.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP 5.7 0.4 - - - -
45A LEU* 3.7 15.9 + - - +
47A SER 3.6 12.3 + - - -
48A PRO* 3.6 43.7 + - + +
49A GLY 3.6 0.6 - - - -
50A SER* 1.3 79.2 - - - +
52A ASP* 1.3 58.2 + - - +
54A ILE* 3.7 2.7 - - + -
55A THR* 2.6 42.9 + - - +
74A TRP* 3.2 31.9 - + - -
78A LEU* 3.2 24.9 - - + -
81A LEU* 3.5 41.3 - - + -
82A LYS* 3.6 37.0 - - + -
85A ARG* 3.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 5.0 4.9 - - - +
50A SER* 3.1 0.6 - - - +
51A TRP* 1.3 79.0 - - - +
53A PRO* 1.3 65.8 - - + +
54A ILE 3.1 0.2 + - - -
55A THR* 3.2 2.9 + - - -
56A ALA* 3.0 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.0 25.3 - - + +
49A GLY 4.6 2.5 - - - +
50A SER* 3.1 28.9 - - - +
52A ASP* 1.3 97.3 - - + +
54A ILE* 1.3 58.3 + - + -
55A THR 3.6 0.2 - - - -
56A ALA* 4.5 4.7 - - + -
57A ALA* 3.6 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.4 25.4 - - + -
38A LEU* 4.1 22.2 - - + +
39A LEU* 3.4 32.8 - - + -
44A ASP 5.7 1.1 - - - +
45A LEU* 5.9 0.7 - - + -
50A SER* 2.9 35.9 - - - +
51A TRP* 3.4 4.2 + - + +
52A ASP 3.0 0.8 - - - -
53A PRO* 1.3 84.1 - - + +
55A THR* 1.3 60.1 + - - +
57A ALA* 4.3 1.7 - - - +
58A LEU* 3.1 26.4 + - + +
74A TRP* 3.4 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TRP* 2.6 23.8 + - - +
52A ASP* 4.0 2.9 - - - -
54A ILE* 1.3 78.9 - - - +
56A ALA* 1.3 64.3 + - - +
57A ALA 3.3 0.2 - - - -
58A LEU* 3.8 1.7 + - - +
59A SER* 3.1 26.9 + - - -
71A LEU* 5.2 4.0 - - + +
74A TRP* 2.7 26.0 + - + +
78A LEU* 3.9 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP 3.0 17.1 + - - +
53A PRO* 5.0 3.4 - - + -
55A THR* 1.3 75.8 - - - +
57A ALA* 1.3 54.4 + - - +
59A SER* 3.6 5.4 - - - -
60A GLN* 2.7 37.1 + - - +
63A MET* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.1 22.9 - - + -
53A PRO 3.6 21.4 + - - +
54A ILE 4.6 1.3 - - - +
55A THR 3.3 0.4 - - - -
56A ALA* 1.3 78.9 - - - +
58A LEU* 1.3 56.8 + - - +
60A GLN* 2.8 17.9 + - - +
61A ARG* 2.8 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A MET* 5.5 1.3 - - + -
32A LEU* 4.3 16.2 - - + -
33A LEU* 4.8 10.8 - - + -
38A LEU* 5.3 3.4 - - + -
54A ILE* 3.1 26.6 + - + +
55A THR 3.8 3.5 + - - +
56A ALA 3.5 0.2 - - - -
57A ALA* 1.3 79.2 - - + +
59A SER* 1.3 57.7 + - - +
61A ARG* 3.3 16.2 - - - +
62A ALA* 3.1 29.1 + - - +
70A GLU* 3.5 33.0 - - + +
71A LEU* 3.8 17.6 - - + +
74A TRP* 3.2 42.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 3.1 20.9 + - - -
56A ALA* 3.6 5.2 - - - -
58A LEU* 1.3 78.3 - - - +
60A GLN* 1.3 57.6 + - - +
62A ALA* 4.0 1.4 - - - +
63A MET* 2.9 42.4 + - - +
71A LEU* 3.6 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA 2.7 17.5 + - - +
57A ALA* 2.8 16.5 + - - +
59A SER* 1.3 77.5 - - - +
61A ARG* 1.3 60.4 + - - +
62A ALA 3.3 0.2 - - - -
63A MET* 3.1 12.6 - - + +
64A ILE* 3.0 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.3 40.6 - - - +
36A GLU* 3.8 9.8 + - - +
57A ALA 2.8 10.6 + - - +
58A LEU* 3.3 25.8 - - - +
60A GLN* 1.3 79.0 - - - +
62A ALA* 1.3 63.7 + - - +
64A ILE* 4.6 2.2 - - - -
65A LEU* 2.7 49.5 + - + +
67A LYS* 3.4 38.8 + - + +
68A SER* 5.8 0.4 - - - +
70A GLU* 3.1 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU 3.1 14.9 + - - +
59A SER 4.2 1.1 - - - +
61A ARG* 1.3 80.2 - - - +
63A MET* 1.3 59.2 + - - +
66A GLY* 2.9 28.9 + - - -
67A LYS 3.2 24.8 + - - +
68A SER* 3.7 22.7 - - - -
71A LEU* 3.7 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA 5.5 0.2 - - - +
59A SER* 2.9 34.6 + - - +
60A GLN* 3.1 22.9 - - + +
62A ALA* 1.3 79.8 - - - +
64A ILE* 1.3 74.1 + - + +
66A GLY* 4.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 3.0 49.2 + - + +
61A ARG* 4.2 2.5 - - - +
63A MET* 1.3 88.1 - - + +
65A LEU* 1.3 76.2 + - + +
66A GLY* 3.1 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 2.7 30.9 + - + +
64A ILE* 1.3 82.1 - - + +
66A GLY* 1.3 58.5 + - - +
67A LYS* 3.7 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA 2.9 15.8 + - - -
63A MET 4.9 2.2 - - - -
64A ILE 3.1 3.7 + - - -
65A LEU* 1.3 79.6 - - - +
67A LYS* 1.3 64.4 + - - +
----------------------------------------------------------
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