Contacts of the helix formed by residues 58 - 73 (chain H) in PDB entry 1RFU
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 58 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H LEU* 1.3 74.9 - - - +
59H SER* 1.3 59.7 + - - +
60H ASP* 2.7 28.9 + - - +
61H GLU* 2.6 50.8 + - - +
62H LEU* 3.0 9.4 + - - +
87H ASP* 3.2 16.4 - - - +
90H PHE* 4.2 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H ASN* 1.3 73.4 - - - +
60H ASP* 1.3 61.8 + - - +
62H LEU* 3.5 3.3 + - - +
63H GLN* 2.9 23.8 + - - +
87H ASP* 4.0 2.8 + - - -
89H SER* 3.0 36.6 + - - -
90H PHE* 4.3 10.9 - - - +
93H MET* 3.1 27.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H ASN* 2.7 24.1 + - - +
59H SER* 1.3 75.4 + - - +
61H GLU* 1.3 63.1 + - + +
63H GLN* 3.2 7.4 + - - +
64H GLU* 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C GLN* 3.6 41.3 + - - +
56H VAL 3.0 26.0 - - - +
57H LEU* 3.0 18.3 - - + -
58H ASN* 2.6 36.8 + - - +
60H ASP* 1.3 73.9 - - + +
62H LEU* 1.3 60.2 + - - +
64H GLU* 3.4 18.3 - - - +
65H LEU* 3.4 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H ILE* 4.9 5.4 - - + -
38H VAL* 3.9 32.8 - - + -
57H LEU* 4.4 1.0 - - - +
58H ASN 3.0 5.4 + - - +
59H SER* 3.8 7.0 - - - +
61H GLU* 1.3 74.2 - - - +
63H GLN* 1.3 67.1 + - - +
65H LEU* 3.2 10.5 + - + +
66H TYR* 2.9 22.4 + - + +
90H PHE* 3.4 38.1 - - + +
93H MET* 3.9 14.6 - - + -
94H VAL* 3.9 19.7 - - + -
97H ILE* 3.8 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H SER 2.9 18.3 + - - +
60H ASP* 3.4 9.9 - - - +
62H LEU* 1.3 76.7 - - - +
64H GLU* 1.3 54.7 + - - +
66H TYR* 3.0 16.1 + - - +
67H ASP* 2.5 74.5 + - - +
93H MET* 2.5 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LYS* 3.4 30.3 - - + +
54C GLY 2.9 26.4 + - - +
55C GLN* 2.6 30.8 - - - +
60H ASP 3.0 14.0 + - - +
61H GLU* 3.4 11.7 - - - +
63H GLN* 1.3 75.4 - - - +
65H LEU* 1.3 52.1 - - - +
67H ASP* 3.3 6.4 + - - +
68H GLY 2.7 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C VAL* 3.8 15.0 - - + -
42C GLN* 3.4 52.0 - - + +
43C PHE 3.6 19.7 - - - -
44C SER* 3.4 10.5 - - - +
53C LYS 4.7 0.2 - - - -
54C GLY* 3.9 7.2 - - - -
55C GLN* 3.6 15.7 - - - +
38H VAL* 3.9 19.1 - - + -
57H LEU* 3.9 4.7 - - + -
61H GLU 3.4 12.1 - - - +
62H LEU* 3.2 10.4 + - + +
64H GLU* 1.3 78.1 - - - +
66H TYR* 1.3 63.9 + - - +
68H GLY* 2.8 12.1 + - - -
69H LEU* 2.9 16.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LEU* 5.1 7.4 - - + -
62H LEU* 2.9 15.8 + - + +
63H GLN* 3.6 19.5 - - - +
65H LEU* 1.3 74.8 - - - +
67H ASP* 1.3 54.0 + - - +
69H LEU* 3.1 19.5 + - + +
70H LYS* 2.5 44.9 + - + +
75H ASN* 3.6 22.7 + - + -
77H TYR* 5.3 1.6 - + - -
97H ILE* 3.5 50.3 + - + +
100H GLU* 3.4 34.2 + - - +
101H LEU* 3.3 30.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LYS* 4.5 16.8 - - + +
63H GLN* 2.5 60.1 + - - +
64H GLU* 3.4 6.8 + - - +
66H TYR* 1.3 73.8 - - - +
68H GLY* 1.3 54.7 + - - +
70H LYS* 3.7 9.0 - - - +
71H LEU* 2.5 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C SER* 3.4 20.9 - - - -
45C ASN* 4.0 0.7 - - - -
52C TRP* 5.1 1.6 - - - -
53C LYS* 4.3 8.7 - - - +
64H GLU 2.7 17.8 + - - -
65H LEU 2.8 5.7 + - - -
67H ASP* 1.3 75.3 - - - +
69H LEU* 1.3 60.9 + - - -
71H LEU* 3.3 12.9 + - - +
72H ASN* 3.3 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C VAL* 3.8 21.3 - - + -
16C ARG* 3.5 32.1 - - + -
44C SER* 3.6 18.5 - - - +
45C ASN* 4.7 1.6 - - - +
8H LEU* 5.0 4.3 - - + -
38H VAL* 5.3 2.5 - - + -
65H LEU 2.9 17.7 + - - +
66H TYR* 3.5 23.6 - - + +
68H GLY* 1.3 70.8 - - - +
70H LYS* 1.3 70.7 + - - +
72H ASN 3.0 2.8 + - - -
73H HIS 3.0 14.2 + - - -
74H VAL* 3.2 27.7 + - + +
75H ASN* 4.4 12.3 - - + +
77H TYR* 3.6 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H TYR* 2.5 26.1 + - + +
67H ASP* 3.1 16.4 - - - +
69H LEU* 1.3 71.8 - - - +
71H LEU* 1.3 57.9 + - + +
73H HIS* 2.6 37.6 + - - +
75H ASN* 3.0 38.5 + - - +
100H GLU* 3.8 13.4 + - - +
104H GLN* 3.7 12.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C HIS* 3.7 48.8 + - + +
53C LYS* 3.6 35.9 - - + +
67H ASP* 2.5 31.8 + - + +
68H GLY* 3.5 8.3 - - - +
70H LYS* 1.3 75.5 - - + +
72H ASN* 1.3 60.4 + - - +
73H HIS* 3.7 16.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ASN* 3.3 23.0 + - - +
49C TYR* 3.5 26.7 - - + +
50C SER* 4.1 4.7 + - - -
51C HIS* 2.9 43.6 + - - +
287C ALA* 5.5 2.8 - - + +
68H GLY 3.3 9.1 + - - +
69H LEU 3.0 1.8 + - - +
70H LYS 3.0 1.2 - - - -
71H LEU* 1.3 75.2 - - - +
73H HIS* 1.3 79.8 + - - +
74H VAL* 3.5 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 73 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H LYS* 2.6 27.2 + - - -
71H LEU* 3.9 14.3 + - - -
72H ASN* 1.3 82.6 - - - +
74H VAL* 1.3 59.9 + - - +
75H ASN* 3.5 10.5 - - - -
76H GLN* 3.4 19.2 - - - +
----------------------------------------------------------
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