Contacts of the helix formed by residues 55 - 72 (chain D) in PDB entry 6CNC
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 LEU 55 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 5.0 13.0 - - + -
53D PRO* 2.8 18.6 + - + +
54D GLU* 1.3 81.4 + - - +
56D GLN* 1.3 64.0 + - - +
57D GLY 2.8 8.1 + - - -
58D ILE* 3.2 43.8 + - + +
59D THR* 3.9 6.4 + - - +
31G ASN* 4.2 29.6 - - + +
35G ALA* 3.9 30.7 - - + -
36G ASN* 5.3 2.2 + - - +
46G ILE 4.4 3.8 - - - +
47G THR* 4.7 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLU* 2.8 37.5 + - - +
27D HIS* 3.4 33.3 + - + +
28D LEU* 3.5 33.0 - - + +
30D ASP* 4.6 1.4 - - - +
53D PRO* 4.8 7.4 - - + +
54D GLU* 3.1 4.4 + - - +
55D LEU* 1.3 82.9 - - - +
57D GLY* 1.3 62.9 + - - +
58D ILE 3.4 0.2 - - - -
59D THR* 3.1 21.3 + - - +
60D ARG* 3.3 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D GLU* 3.4 10.3 + - - -
55D LEU 2.8 4.8 + - - -
56D GLN* 1.3 78.6 - - - +
58D ILE* 1.3 54.1 + - - -
60D ARG* 3.9 2.9 + - - +
61D ASN* 2.7 37.8 + - - +
36G ASN* 5.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 5.7 6.3 - - + -
55D LEU* 3.2 36.0 + - + +
57D GLY* 1.3 70.5 - - - +
59D THR* 1.3 82.9 + - - +
61D ASN* 2.9 11.4 + - + +
62D VAL* 2.7 40.8 + - + +
35G ALA 5.4 0.2 - - - -
36G ASN* 3.0 42.7 - - - +
46G ILE* 3.7 41.3 - - + +
47G THR* 5.3 3.8 - - - -
103G GLY 5.6 1.6 - - - +
104G ILE* 6.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 5.1 10.9 - - + +
23D LEU* 6.1 1.4 - - - +
24D GLU* 3.3 33.6 + - + +
30D ASP* 3.4 19.5 - - - +
55D LEU* 4.0 6.6 + - - +
56D GLN* 3.1 24.8 + - - +
58D ILE* 1.3 95.6 - - - +
60D ARG* 1.3 62.2 + - - +
61D ASN 3.0 0.3 + - - -
62D VAL* 4.6 0.8 - - - +
63D VAL* 3.0 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ASP* 3.7 38.8 + - - +
31D GLN* 3.0 47.9 - - - +
56D GLN* 3.3 16.2 + - + +
57D GLY 4.4 2.9 - - - +
59D THR* 1.3 78.9 - - - +
61D ASN* 1.3 65.5 + - - +
63D VAL* 3.3 19.4 - - - +
64D ASN* 3.6 10.2 + - - +
102G LEU* 5.7 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D GLY* 2.7 27.8 + - - +
58D ILE* 2.9 14.2 + - + +
60D ARG* 1.3 77.7 - - - +
62D VAL* 1.3 63.7 + - + +
64D ASN* 2.9 28.4 + - - +
65D TYR 4.1 1.6 + - - -
36G ASN* 5.8 0.2 + - - -
101G LEU* 5.6 2.3 - - - +
102G LEU* 4.3 14.4 - - - +
103G GLY* 2.4 51.4 + - - +
104G ILE* 4.4 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ASP* 5.2 2.9 - - - +
20D LEU* 4.2 23.6 - - + -
58D ILE* 2.7 28.3 + - + +
59D THR* 4.6 0.7 - - - +
61D ASN* 1.3 75.0 - - + +
63D VAL* 1.3 60.8 + - - +
64D ASN 3.1 0.9 + - - -
65D TYR* 4.0 0.9 + - - +
66D LEU* 3.3 41.5 + - + +
2G PHE* 6.4 1.8 - - + -
46G ILE* 4.6 26.7 - - + -
101G LEU* 6.2 2.9 - - - -
104G ILE* 5.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 3.6 29.3 - - + +
20D LEU* 5.5 3.9 - - + +
21D THR* 4.7 9.4 - - - +
30D ASP* 5.0 14.8 - - - +
59D THR* 3.0 29.0 + - + +
60D ARG* 3.3 23.8 - - - +
62D VAL* 1.3 77.5 - - - +
64D ASN* 1.3 69.2 + - - +
66D LEU* 4.1 0.5 - - - +
67D SER* 3.2 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D ARG 3.6 10.8 - - - +
61D ASN* 2.9 18.1 + - - +
62D VAL 3.1 0.4 - - - -
63D VAL* 1.3 87.0 - - - +
65D TYR* 1.3 67.3 + - - +
67D SER* 2.9 10.4 + - - -
68D ILE* 3.2 19.8 + - - +
102G LEU* 3.3 43.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ASN 4.1 1.4 + - - -
62D VAL 4.0 2.8 + - - +
64D ASN* 1.3 83.5 - - + +
66D LEU* 1.3 74.3 + - + +
67D SER 3.1 1.0 + - - -
68D ILE* 3.2 25.2 + - + -
69D ASN* 2.4 56.3 + - + +
125D ASN* 6.5 0.9 - - + -
126D GLN* 3.5 11.9 + - - -
85G VAL* 5.2 5.4 - - + -
86G THR* 2.4 46.3 + - + -
101G LEU* 4.5 28.7 - - + -
102G LEU* 6.2 0.9 - - + -
145G LYS* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ASP* 3.3 41.1 - - + +
17D LEU* 3.5 44.6 - - + +
20D LEU* 5.5 1.8 - - + -
62D VAL* 3.3 33.4 + - + +
64D ASN 3.3 0.2 - - - -
65D TYR* 1.3 87.0 - - + +
67D SER* 1.3 59.7 + - - +
70D LYS* 3.4 24.1 + - - +
98D MET* 4.1 1.9 - - - +
2G PHE* 5.7 7.0 - - + -
101G LEU* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 4.0 8.7 - - - +
63D VAL* 3.2 21.1 + - - -
64D ASN* 2.9 6.2 + - - -
66D LEU* 1.3 77.8 - - - +
68D ILE* 1.3 64.2 + - - +
69D ASN 3.6 0.2 - - - -
70D LYS* 3.4 16.8 - - - +
71D ASN* 3.3 22.3 + - - +
98D MET* 5.1 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ASN* 3.2 12.5 + - - +
65D TYR* 3.6 34.3 - - + +
67D SER* 1.3 77.1 - - - +
69D ASN* 1.3 58.3 + - - +
71D ASN* 2.9 10.2 + - + +
72D PHE* 2.4 65.5 + - + +
145G LYS* 5.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D TYR* 2.4 55.1 + - + +
68D ILE* 1.3 81.5 - - - +
70D LYS* 1.3 64.3 + - + +
72D PHE 3.1 28.0 - - - +
125D ASN 5.2 8.5 + - - -
126D GLN* 4.1 12.1 + - - +
127D LEU 5.6 0.8 - - - +
128D PRO* 5.1 12.1 - - - +
86G THR* 4.2 1.0 + - - -
145G LYS* 4.1 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ASP 4.7 12.4 + - - -
14D TYR* 4.9 8.9 + - - -
66D LEU 3.4 20.2 + - - +
67D SER 3.4 9.0 - - - +
69D ASN* 1.3 80.9 - - + +
71D ASN* 1.3 63.3 + - - +
98D MET* 3.2 33.2 - - + +
124D VAL* 4.4 13.8 + - - +
125D ASN* 5.0 11.0 - - - +
160D TYR* 2.7 44.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D SER* 3.3 24.8 + - - +
68D ILE* 2.9 12.2 + - + +
70D LYS* 1.3 79.5 - - - +
72D PHE* 1.3 90.5 + - + +
98D MET* 5.3 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ILE* 2.4 45.1 + - + +
69D ASN* 3.1 31.4 + - - -
71D ASN* 1.3 92.4 - - + +
145G LYS* 2.4 37.3 + - - +
----------------------------------------------------------
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