Contacts of the helix formed by residues 57 - 75 (chain C) in PDB entry 4H7Y
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 ASN 57 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO* 3.5 16.5 - - - +
14C GLU* 2.9 28.2 + - - +
54C TYR* 3.0 31.5 + - + +
55C GLY 3.4 0.5 - - - +
56C GLN* 1.3 78.4 - - - +
58C GLU* 1.3 63.2 + - - +
59C SER* 2.8 33.3 + - - -
60C PHE* 2.9 15.4 + - + +
61C ALA* 3.0 20.6 + - - +
90C CYS* 5.5 0.2 - - - -
93C PHE* 3.8 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLN 3.6 4.0 + - - -
57C ASN* 1.3 73.7 + - - +
59C SER* 1.3 58.6 + - - +
61C ALA* 3.3 2.8 + - - +
62C ARG* 3.0 41.7 + - + +
93C PHE* 3.6 33.4 - - + -
95C PHE* 4.4 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO* 3.9 25.8 - - - -
14C GLU* 3.7 19.8 + - - +
17C LEU* 3.9 23.3 - - - +
57C ASN* 2.8 9.4 + - - -
58C GLU* 1.3 78.7 - - - +
60C PHE* 1.3 62.7 + - - +
62C ARG* 3.2 5.4 + - - +
63C ILE* 3.0 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO* 3.6 9.1 - - + +
46C ILE* 5.4 5.2 - - + -
49C LEU* 3.6 40.8 - - + -
51C PRO* 3.8 27.4 - - + -
54C TYR* 3.3 41.1 - + + +
57C ASN* 2.9 16.1 + - - +
59C SER* 1.3 78.2 - - - +
61C ALA* 1.3 57.2 + - - +
63C ILE* 3.2 8.6 + - + +
64C GLN* 2.9 58.7 + - + +
89C ASN* 4.1 9.4 - - + -
90C CYS* 3.6 23.8 - - - -
----------------------------------------------------------
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 ASN 3.0 8.9 + - - +
58C GLU 3.3 8.5 + - - +
60C PHE* 1.3 77.9 - - - +
62C ARG* 1.3 56.6 + - - +
64C GLN* 3.8 0.5 - - - +
65C VAL* 2.9 35.2 + - - +
90C CYS* 3.7 24.7 - - + -
93C PHE* 3.6 30.3 - - + -
95C PHE* 3.6 13.9 - - + -
96C VAL* 4.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 3.6 35.0 - - + +
21C LEU* 4.0 29.9 - - - +
58C GLU* 3.0 25.9 + - + +
59C SER* 3.2 8.9 + - - +
61C ALA* 1.3 75.1 - - - +
63C ILE* 1.3 59.2 + - - +
65C VAL* 4.1 1.2 - - - +
66C ARG* 2.9 33.3 + - - +
95C PHE* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO* 3.6 26.0 - - + +
16C TRP* 4.0 11.4 - - + -
17C LEU* 4.0 12.1 - - + +
20C LEU* 4.1 11.2 - - + -
42C TYR* 3.5 23.2 - - + -
45C ALA* 4.2 12.1 - - + -
46C ILE* 4.0 20.9 - - + +
49C LEU* 3.8 25.6 - - + -
59C SER 3.0 13.6 + - - +
60C PHE* 3.2 11.0 + - + +
62C ARG* 1.3 76.5 - - - +
64C GLN* 1.3 63.3 + - + +
67C PHE* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B SER* 5.5 0.2 + - - -
44B GLN* 6.1 0.2 - - - +
47B GLU* 3.6 20.3 + - - +
46C ILE* 4.0 23.2 + - + +
51C PRO* 4.9 2.2 - - - +
60C PHE* 2.9 54.6 + - + +
61C ALA 3.8 3.6 - - - +
63C ILE* 1.3 75.9 - - + +
65C VAL* 1.3 63.5 + - - +
67C PHE* 3.6 7.8 + - - +
68C ALA* 3.3 20.4 + - - +
82C TYR 4.5 1.6 - - - +
85C MET 3.5 1.4 - - - +
86C ALA* 3.5 32.2 + - + +
89C ASN* 3.0 29.3 + - - +
90C CYS* 4.0 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA 2.9 20.4 + - - +
62C ARG 4.1 2.2 - - - +
64C GLN* 1.3 76.3 - - - +
66C ARG* 1.3 66.1 + - + +
68C ALA* 3.2 6.5 + - - +
69C GLU* 3.0 33.9 + - - +
83C PHE* 6.0 1.1 - - + -
86C ALA* 4.4 6.5 - - + -
95C PHE* 3.8 15.9 - - + -
96C VAL* 3.6 42.8 - - + +
99C SER* 3.3 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 6.4 0.7 - - + -
24C GLU* 2.8 36.0 + - - +
30C LEU* 5.7 2.2 - - - +
42C TYR* 3.2 31.6 - - + +
62C ARG 2.9 19.3 + - - +
65C VAL* 1.3 77.5 - - - +
67C PHE* 1.3 57.4 + - - +
69C GLU* 2.9 37.7 + - - +
70C LEU* 2.9 52.2 + - + +
73C ILE* 4.4 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU* 3.6 36.3 - - + -
39C ILE* 3.9 21.1 - - + -
42C TYR* 3.7 28.8 - - + -
43C SER* 3.4 26.2 - - - -
46C ILE* 3.4 25.4 - - + -
63C ILE 3.1 18.2 + - - +
64C GLN 3.8 2.9 - - - +
65C VAL 3.2 0.2 - - - -
66C ARG* 1.3 78.9 - - - +
68C ALA* 1.3 57.3 + - - +
70C LEU* 3.3 4.1 + - - +
71C LYS* 2.9 49.6 + - + +
82C TYR* 3.7 28.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLN 3.3 6.5 + - - +
65C VAL* 3.2 11.3 + - - +
67C PHE* 1.3 79.4 - - - +
69C GLU* 1.3 57.6 + - - +
71C LYS* 3.3 3.2 + - - +
72C ALA* 3.0 28.4 + - - +
79C ALA* 4.5 0.3 - - - +
82C TYR* 3.7 38.6 - - + +
83C PHE* 3.5 30.8 - - + -
86C ALA* 5.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C VAL* 3.0 26.7 + - - +
66C ARG* 2.9 43.8 + - - +
68C ALA* 1.3 77.4 - - - +
70C LEU* 1.3 57.2 + - - +
72C ALA* 3.2 5.2 + - - +
73C ILE* 3.0 33.9 + - + +
83C PHE* 4.1 10.3 - - + -
99C SER* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLU* 4.7 0.4 - - - +
30C LEU* 4.8 4.3 - - + -
35C LEU* 3.8 19.9 - - + +
38C LEU* 3.7 32.3 - - + -
39C ILE* 3.6 23.5 - - + +
42C TYR* 3.8 29.6 - - + -
66C ARG* 2.9 49.9 + - + +
67C PHE* 3.7 4.9 - - - +
69C GLU* 1.3 73.9 - - - +
71C LYS* 1.3 61.9 + - - +
73C ILE* 3.4 12.5 + - + +
74C GLN* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU 5.7 0.2 - - - -
50B PRO* 5.2 8.7 - - - +
39C ILE* 3.7 30.3 - - + +
67C PHE* 2.9 40.6 + - + +
68C ALA 3.3 3.3 + - - +
70C LEU* 1.3 76.1 - - - +
72C ALA* 1.3 58.1 + - - +
74C GLN* 3.3 26.2 + - - +
75C GLU* 2.8 31.7 + - - +
79C ALA* 3.9 2.0 - - + -
82C TYR* 3.5 52.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ALA 3.0 16.7 + - - +
69C GLU* 3.2 6.2 + - - +
71C LYS* 1.3 74.2 - - - +
73C ILE* 1.3 64.8 + - + +
76C PRO* 3.1 29.1 - - + +
79C ALA* 3.6 12.5 - - + +
83C PHE* 3.9 5.2 - - + -
103C PHE* 3.8 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 5.5 6.7 - - + -
35C LEU* 3.9 19.0 - - + +
66C ARG* 4.4 14.4 - - - +
69C GLU* 3.0 16.6 + - + +
70C LEU* 3.5 26.2 - - + +
72C ALA* 1.3 78.9 - - - +
74C GLN* 1.3 60.5 - - - +
76C PRO* 4.3 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 4.0 16.4 - - + +
36C ASN* 2.9 37.9 + - - +
39C ILE* 3.6 18.0 - - + +
70C LEU 3.1 17.3 + - - +
71C LYS* 3.3 33.1 + - - +
73C ILE* 1.3 79.3 - - - +
75C GLU* 1.3 67.8 + - + +
76C PRO* 4.2 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 4.7 8.7 - - - +
71C LYS 2.8 19.2 + - - +
74C GLN* 1.3 83.2 - - + +
76C PRO* 1.3 75.4 - - - +
77C ASP* 2.9 37.5 + - - +
78C ASP* 3.2 28.6 + - + +
79C ALA* 3.5 7.4 + - - +
----------------------------------------------------------
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