Contacts of the helix formed by residues 40 - 65 (chain C) in PDB entry 5CVA
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 40 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLU 3.6 3.0 + - - -
39C ALA* 1.3 78.1 - - - +
41C GLU* 1.3 65.0 + - - +
42C GLN* 3.6 17.3 + - - +
43C ARG* 3.1 25.9 + - - +
44C ILE* 3.1 20.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 4.1 26.3 - - + +
50B LYS* 3.0 28.6 + - - -
40C SER* 1.3 72.4 - - - +
42C GLN* 1.3 67.4 + - - +
44C ILE* 3.2 3.6 + - - +
45C ARG* 2.7 77.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C SER* 3.2 16.3 - - - +
41C GLU* 1.3 93.4 + - - +
43C ARG* 1.3 57.1 + - - +
45C ARG* 3.4 10.3 + - - +
46C GLU* 2.9 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 5.7 3.0 - - - +
39A PRO* 2.8 28.3 + - - +
40A THR* 3.6 2.0 - - - +
41A ASP* 2.8 36.6 + - - +
44A ILE* 3.7 10.6 - - + +
39C ALA* 3.5 24.8 - - + +
40C SER* 3.1 24.4 + - - +
42C GLN* 1.3 75.0 - - - +
44C ILE* 1.3 60.9 + - - +
46C GLU* 3.4 5.1 + - - +
47C LEU* 3.0 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 4.2 16.2 - - + -
48A CYS* 4.3 21.3 - - - -
43B HIS* 3.7 28.9 - - + +
44B ILE* 3.9 18.4 - - + +
47B VAL* 3.7 29.6 - - + -
48B ALA 4.6 1.6 - - - +
51B MET* 4.6 1.8 - - - -
39C ALA* 3.9 23.1 - - + +
40C SER 3.1 16.6 + - - +
41C GLU 3.6 5.2 - - - +
43C ARG* 1.3 73.7 - - - +
45C ARG* 1.3 66.8 + - - +
47C LEU 3.2 1.0 + - - -
48C CYS* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 4.0 3.6 - - + +
50B LYS* 4.4 15.4 - - - +
51B MET* 3.6 33.8 - - + +
54B GLU* 2.8 43.6 + - - -
41C GLU* 2.7 55.1 + - - +
42C GLN* 3.7 10.3 - - - +
44C ILE* 1.3 73.3 - - - +
46C GLU* 1.3 59.6 + - + +
49C GLY* 2.9 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLN* 2.9 22.7 + - + +
43C ARG* 3.7 7.0 - - - +
45C ARG* 1.3 78.3 - - + +
47C LEU* 1.3 64.2 + - + +
48C CYS 3.6 0.3 + - - -
49C GLY* 4.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 3.6 44.6 - - + +
44A ILE* 3.7 38.4 - - + -
45A LYS* 3.8 42.7 - - + +
43C ARG* 3.0 27.2 + - + +
44C ILE 3.2 2.9 + - - +
46C GLU* 1.3 81.7 - - + +
48C CYS* 1.3 59.9 + - - +
50C GLY 5.3 1.1 + - - -
51C MET* 4.5 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.9 16.6 - - - -
45A LYS* 4.3 5.8 - - - -
48A CYS* 2.0 54.5 - - + -
51B MET* 3.8 10.1 - - + -
44C ILE* 3.0 16.8 + - - +
47C LEU* 1.3 81.1 - - - +
49C GLY* 1.3 66.1 + - - +
50C GLY 3.3 2.2 - - - -
51C MET* 3.3 8.9 + - - +
52C ILE* 3.1 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B MET* 3.4 14.1 - - - +
55B GLN* 3.5 10.3 + - - -
45C ARG 2.9 19.9 + - - -
46C GLU 4.3 1.4 + - - -
47C LEU 3.7 0.4 - - - -
48C CYS* 1.3 77.5 - - - +
50C GLY* 1.3 61.4 + - - +
53C SER* 3.2 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU 5.3 1.8 + - - -
47C LEU 5.3 1.0 + - - -
48C CYS 3.3 0.4 - - - -
49C GLY* 1.3 72.8 - - - +
51C MET* 1.3 60.1 + - - +
53C SER* 3.2 6.5 + - - -
54C GLU* 2.9 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 3.6 42.4 - - + +
48A CYS* 4.0 8.7 - - + -
49A MSE 3.7 44.4 - - + +
52A ILE* 3.7 12.1 - - + -
47C LEU 4.5 7.5 + - - +
48C CYS* 3.3 9.6 + - - +
50C GLY* 1.3 77.8 - - - +
52C ILE* 1.3 62.4 + - - +
54C GLU* 3.5 11.3 + - - +
55C GLN* 3.1 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A CYS* 5.4 1.6 - - + -
52A ILE* 3.8 26.2 - - + -
59A MSE 4.9 0.2 - - - +
48B ALA* 4.1 17.3 - - + +
51B MET* 3.6 37.0 - - + -
52B LEU* 3.8 29.8 - - + +
55B GLN* 3.7 20.6 - - - +
48C CYS* 3.1 25.5 + - + +
49C GLY 3.9 4.0 - - - +
51C MET* 1.3 76.8 - - + +
53C SER* 1.3 57.9 + - - +
55C GLN* 3.5 1.4 + - - +
56C ILE* 3.1 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLN* 2.7 25.0 + - - -
49C GLY 3.2 12.6 + - - -
50C GLY* 3.2 11.1 + - - -
52C ILE* 1.3 74.9 - - - +
54C GLU* 1.3 60.8 + - - +
56C ILE* 3.3 4.4 + - - +
57C ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLY* 2.9 22.5 + - - +
51C MET* 3.9 10.6 - - - +
53C SER* 1.3 75.5 - - - +
55C GLN* 1.3 63.6 + - - +
57C ALA* 3.2 6.4 + - - +
58C GLN* 2.8 46.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MSE 4.2 26.7 - - - +
52A ILE* 3.8 32.0 - - + +
56A PHE* 4.0 20.3 - - - -
59A MSE 4.0 8.0 - - + +
51C MET* 3.1 24.5 + - + +
52C ILE 3.8 4.0 - - - +
54C GLU* 1.3 81.3 + - - +
56C ILE* 1.3 62.7 + - - +
58C GLN* 3.9 21.1 + - - +
59C LEU* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A MSE 3.7 21.1 - - + -
63A LEU* 3.8 19.4 - - + +
52B LEU* 4.0 9.2 - - + -
55B GLN* 3.7 34.1 - - + +
56B LEU* 4.1 17.5 - - + +
59B VAL* 3.9 24.2 - - + -
52C ILE* 3.1 30.2 + - + +
53C SER* 3.7 4.3 - - - +
55C GLN* 1.3 75.3 - - - +
57C ALA* 1.3 58.5 + - - +
59C LEU* 3.2 1.9 + - - +
60C ALA* 2.8 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C SER 2.9 17.5 + - - +
54C GLU* 3.4 8.5 - - - +
56C ILE* 1.3 78.1 - - - +
58C GLN* 1.3 64.2 + - + +
60C ALA* 3.3 5.0 + - - +
61C ALA* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLU* 2.8 31.6 + - - +
55C GLN* 3.9 24.2 + - - +
57C ALA* 1.3 74.0 - - + +
59C LEU* 1.3 57.9 + - - +
61C ALA* 3.6 6.9 - - - +
62C HIS* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 3.8 39.0 - - + +
59A MSE 3.6 22.0 - - + -
60A ALA* 3.6 31.9 - - + +
63A LEU* 3.8 10.8 - - + -
55C GLN 3.0 20.2 + - - +
56C ILE* 3.7 3.1 - - - +
58C GLN* 1.3 73.7 - - - +
60C ALA* 1.3 66.4 + - - +
62C HIS* 3.3 10.6 + - + -
63C LEU* 3.1 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 4.0 32.2 - - + +
59B VAL* 5.7 2.0 - - + -
56C ILE* 2.8 18.1 + - + +
57C ALA* 3.8 5.2 - - - +
59C LEU* 1.3 76.2 - - - +
61C ALA* 1.3 63.6 + - - +
63C LEU* 3.2 13.0 + - - +
64C ARG* 3.3 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ALA 3.0 16.9 + - - +
58C GLN* 3.6 8.3 - - - +
60C ALA* 1.3 77.3 - - - +
62C HIS* 1.3 62.7 + - - +
64C ARG* 3.2 15.2 + - - +
65C LYS* 3.3 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLN 3.0 18.1 + - - +
59C LEU* 3.6 13.5 - - + +
61C ALA* 1.3 76.3 - - - +
63C LEU* 1.3 73.2 + - + +
64C ARG 3.2 1.5 + - - -
65C LYS* 3.3 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA* 3.6 40.8 - - + +
63A LEU* 3.9 24.2 - - + +
64A LYS* 4.1 6.7 - - + +
65A ARG* 3.8 21.9 + - - +
59C LEU* 3.1 35.1 + - + +
60C ALA 3.2 5.1 + - - +
62C HIS* 1.3 87.3 - - + +
64C ARG* 1.3 59.0 + - - +
65C LYS 3.5 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 3.8 27.8 + - + +
60C ALA 3.3 12.4 + - - +
61C ALA* 3.2 8.3 + - - +
63C LEU* 1.3 77.9 - - - +
65C LYS* 1.3 67.7 + - - +
66C PRO* 3.8 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 3.2 12.8 + - - -
61C ALA* 3.3 13.2 + - - +
62C HIS* 3.3 49.6 + - + +
63C LEU 3.5 1.2 - - - +
64C ARG* 1.3 81.5 - - - +
66C PRO* 1.3 72.2 - - + +
67C LEU 3.7 3.1 - - - +
----------------------------------------------------------
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