Contacts of the helix formed by residues 46 - 66 (chain E) in PDB entry 6VVT
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 46 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989D ASP* 3.1 31.2 - - - -
990D ILE* 4.6 1.3 - - - -
1268D TYR* 2.7 40.0 + - - -
41E LEU* 4.4 6.2 - - - +
44E ALA* 4.4 2.3 - - - +
45E SER* 1.3 82.3 + - - +
47E LYS* 1.3 65.1 + - - +
48E TYR* 3.4 9.6 + - - -
49E ALA* 3.1 2.8 + - - +
50E LEU* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070C TYR 5.3 1.9 + - - -
506D ARG* 4.4 12.1 - - - +
557D ILE* 3.8 7.3 - - + +
558D LEU* 3.8 23.6 - - + +
984D THR* 3.7 24.8 - - + +
989D ASP* 3.0 23.0 + - - +
992D GLU* 3.0 23.5 + - - -
37E ILE* 6.4 0.2 - - + -
41E LEU* 3.7 27.8 - - + +
46E SER* 1.3 72.6 - - - +
48E TYR* 1.3 91.9 + - + +
50E LEU* 3.4 5.1 + - - +
51E VAL* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070C TYR 3.3 25.6 + - - -
1071C GLY* 3.9 2.4 - - - -
506D ARG* 5.4 0.2 + - - -
558D LEU* 4.0 15.7 - - + -
989D ASP* 3.7 20.0 - - + -
991D GLY* 3.8 2.9 - - - -
992D GLU* 2.5 55.9 + - - +
1262D GLY* 3.5 30.3 - - - -
1263D THR* 3.8 6.1 - - + +
1268D TYR* 3.7 28.9 - + + -
46E SER* 3.0 11.8 - - - +
47E LYS* 1.3 88.4 - - + +
49E ALA* 1.3 66.1 + - - +
51E VAL* 2.9 23.5 + - - +
52E ILE* 3.3 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1268D TYR* 3.6 20.7 - - + -
1271D ILE* 3.8 15.2 - - + +
44E ALA* 4.3 3.6 - - + -
45E SER* 3.3 31.0 - - - +
46E SER* 3.1 9.3 + - - +
48E TYR* 1.3 78.2 - - - +
50E LEU* 1.3 56.6 + - - +
52E ILE* 3.5 1.0 + - - +
53E TYR* 2.7 31.9 + - - +
103E HIS* 4.6 0.7 - - + -
105E GLU* 3.7 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557D ILE* 3.9 24.2 - - + -
37E ILE* 4.7 3.1 - - + +
40E LEU* 3.4 43.1 - - + +
41E LEU* 3.6 23.3 - - + -
44E ALA* 4.1 10.4 - - + +
46E SER 3.0 11.2 + - - +
47E LYS* 3.4 11.0 - - - +
48E TYR 3.1 0.2 - - - -
49E ALA* 1.3 78.0 - - - +
51E VAL* 1.3 61.5 + - - +
53E TYR* 3.2 4.8 - - + +
54E ALA* 3.0 17.7 + - - +
93E LEU* 4.5 10.3 - - + -
96E ILE* 4.2 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D GLU* 4.0 3.6 - - + +
553D ALA* 3.5 25.8 - - + +
554D GLU* 3.7 22.2 - - + +
557D ILE* 3.8 18.4 - - + -
558D LEU* 3.4 30.1 - - + -
1263D THR* 3.9 9.9 - - + -
47E LYS 3.2 15.3 - - - +
48E TYR* 2.9 10.9 + - - +
50E LEU* 1.3 77.9 - - - +
52E ILE* 1.3 57.5 + - + +
54E ALA* 3.1 0.3 + - - -
55E ALA* 2.7 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074C TYR* 3.4 42.0 - - + +
550D GLU* 4.5 8.7 - - + -
1263D THR* 4.1 15.5 - - + +
1268D TYR* 3.1 34.3 - - + +
1269D ARG* 4.1 4.3 - - - -
1271D ILE* 4.2 9.6 - - + -
1273D VAL* 4.5 0.7 - - - +
48E TYR 3.3 10.3 + - - +
49E ALA 4.1 3.6 - - - +
51E VAL* 1.3 76.9 - - + +
53E TYR* 1.3 66.1 + - - +
55E ALA* 4.0 3.4 - - - -
56E LYS* 3.1 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271D ILE* 4.7 4.6 - - - +
1273D VAL* 3.3 32.9 - - + +
43E ARG* 4.0 10.8 + - + -
44E ALA* 4.0 10.3 - - + -
49E ALA 2.7 24.1 + - - +
50E LEU* 3.2 8.5 - - - +
52E ILE* 1.3 75.7 - - - +
54E ALA* 1.3 60.5 + - - +
57E ARG* 3.6 8.1 + - - +
96E ILE* 3.6 32.0 - - + +
101E LEU* 2.6 52.6 + - + -
102E GLU* 3.4 8.7 - - - -
103E HIS* 3.4 52.3 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D ALA* 5.2 2.9 - - + -
557D ILE* 5.3 0.7 - - + -
50E LEU 3.0 14.7 + - - +
51E VAL 4.1 1.6 - - - +
53E TYR* 1.3 75.2 - - - +
55E ALA* 1.3 58.6 + - - +
57E ARG* 3.3 0.6 + - - -
58E ALA* 2.9 30.8 + - - +
89E LEU* 3.8 12.1 - - + +
92E ALA* 3.6 14.0 - - + +
93E LEU* 3.6 30.7 - - + -
96E ILE* 3.7 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D ALA* 3.8 4.6 - - - +
550D GLU* 3.6 42.8 - - + +
553D ALA* 4.3 1.6 - - + -
51E VAL* 2.7 23.9 + - + +
52E ILE* 3.3 7.6 + - + +
54E ALA* 1.3 72.3 - - - +
56E LYS* 1.3 65.0 + - + +
58E ALA* 3.1 6.2 + - - +
59E ARG* 3.0 26.0 + - - +
89E LEU* 4.4 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074C TYR* 5.8 2.0 - - - -
550D GLU* 4.9 9.6 - - + +
1269D ARG 3.0 28.2 + - - -
1270D ASN* 4.0 5.1 - - - +
1271D ILE 2.9 29.7 + - - +
1272D GLN* 5.4 0.8 - - - +
1273D VAL* 4.2 13.7 - - + +
52E ILE* 3.1 26.7 + - + +
55E ALA* 1.3 79.7 - - + +
57E ARG* 1.3 57.6 + - - +
59E ARG* 3.2 13.8 + - + +
60E GLN* 2.9 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1273D VAL* 3.5 30.1 - - + +
1275D PRO* 4.8 2.6 - - - +
53E TYR 3.6 9.4 + - - +
54E ALA* 3.3 8.3 + - - +
55E ALA 3.2 1.2 - - - -
56E LYS* 1.3 75.3 - - - +
58E ALA* 1.3 60.0 + - - +
60E GLN* 2.9 38.8 + - - +
61E ILE* 2.9 46.4 + - - +
76E VAL* 3.3 34.5 + - - +
77E GLY* 3.4 16.4 - - - -
79E LEU* 3.6 16.3 - - - +
92E ALA* 3.7 12.8 - - + -
95E GLU* 2.4 31.6 + - - +
101E LEU* 3.8 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D ALA* 4.1 10.8 - - + -
54E ALA 2.9 14.1 + - - +
55E ALA 3.1 8.9 + - - +
57E ARG* 1.3 75.2 - - - +
59E ARG* 1.3 62.6 + - - +
61E ILE* 3.3 3.2 + - - +
62E ASN* 3.0 25.7 + - - +
88E PRO* 4.0 15.6 - - + +
89E LEU* 3.7 38.6 - - + +
92E ALA* 3.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102C ASN* 3.4 31.2 + - - +
1103C ILE 3.1 34.0 + - - +
1104C PRO* 5.0 3.2 - - - +
1105C GLU* 5.4 1.0 - - - +
1202C EDO 3.8 34.3 + - - +
548D SER* 4.4 10.5 - - - -
549D ALA* 3.7 19.3 - - - +
550D GLU* 3.4 27.6 + - - +
55E ALA 3.0 16.5 + - - +
56E LYS* 3.2 14.3 + - + +
58E ALA* 1.3 74.5 - - - +
60E GLN* 1.3 63.4 + - - +
62E ASN 3.7 0.2 + - - -
63E ASP* 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1273D VAL* 2.9 37.3 + - - +
1274D GLN* 5.1 0.8 - - - +
1275D PRO* 4.8 1.6 - - - +
56E LYS* 2.9 15.9 + - + +
57E ARG* 2.9 33.9 + - - +
59E ARG* 1.3 75.8 - - - +
61E ILE* 1.3 66.0 + - - +
63E ASP* 3.2 10.3 + - - +
64E TYR* 3.1 17.0 + - - +
75E TYR* 3.8 10.6 - - + +
76E VAL* 4.2 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E ARG* 2.9 52.4 + - - +
58E ALA 3.3 3.8 + - - +
60E GLN* 1.3 75.0 - - - +
62E ASN* 1.3 59.7 + - - +
64E TYR* 2.8 25.6 + - - +
65E TYR* 3.1 22.9 + - + -
76E VAL 4.6 3.6 - - - +
78E PRO* 4.2 22.4 - - + -
88E PRO* 3.9 25.1 - - + +
91E ILE* 3.4 37.5 - - + -
92E ALA 4.2 1.3 - - - +
95E GLU* 3.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100C GLY 2.7 28.3 + - - +
1101C GLU* 4.1 4.2 - - - -
1102C ASN* 3.7 20.3 - - - +
58E ALA 3.0 15.8 + - - +
61E ILE* 1.3 79.0 - - - +
63E ASP* 1.3 60.9 + - - +
65E TYR* 3.5 12.8 + - - +
66E ASN* 3.2 26.7 + - - +
88E PRO* 3.9 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102C ASN* 2.9 25.7 + - - -
1202C EDO 4.0 9.8 - - - -
59E ARG 3.0 21.7 + - - +
60E GLN* 3.4 12.3 - - - +
62E ASN* 1.3 77.2 - - - +
64E TYR* 1.3 62.3 + - - +
66E ASN* 2.9 23.4 + - - +
67E GLN 5.5 1.6 - - - +
68E LEU* 2.9 31.8 - - + +
69E GLY* 5.3 4.5 - - - -
75E TYR* 4.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E GLN 3.1 7.0 + - - +
61E ILE* 2.8 13.1 + - - +
63E ASP* 1.3 75.9 - - - +
65E TYR* 1.3 92.3 + + - +
66E ASN 2.6 18.4 - - - +
68E LEU* 4.1 1.1 - - - -
75E TYR* 3.2 33.8 - - + +
76E VAL 4.4 2.0 - - - +
77E GLY 3.0 28.3 - - - +
78E PRO* 3.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ILE* 3.1 18.3 + - + -
62E ASN* 3.9 16.8 - - - +
63E ASP 3.3 0.2 - - - -
64E TYR* 1.3 106.8 - + - +
66E ASN* 1.3 64.9 + - - +
78E PRO* 3.3 24.8 - - + +
82E PRO* 3.9 14.9 - - - +
86E GLU 5.7 3.8 - - - -
88E PRO* 6.1 5.6 - - + -
91E ILE* 4.4 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099C LYS 4.7 4.3 + - - +
1100C GLY 3.7 21.4 + - - +
1101C GLU* 4.0 22.2 - - - +
62E ASN* 3.2 17.9 + - - +
63E ASP* 2.9 17.2 + - - +
64E TYR 2.6 22.3 - - - +
65E TYR* 1.3 84.0 - - - +
67E GLN* 1.3 63.3 + - - +
68E LEU 3.5 1.4 + - - -
----------------------------------------------------------
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