Contacts of the helix formed by residues 66 - 76 (chain C) in PDB entry 1R1P
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 66 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLY 3.5 1.8 + - - -
65C LEU* 1.3 76.5 - - - +
67C ARG* 1.3 59.4 + - - +
68C HIS* 3.5 6.8 + - - +
69C GLN* 2.9 42.6 + - - +
70C ALA* 2.9 29.6 + - - +
85C ARG* 4.1 1.8 - - - +
88C GLN* 3.7 26.0 - - - -
55D ILE* 6.2 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C SER* 1.3 73.3 - - - +
68C HIS* 1.3 69.9 + - + +
70C ALA* 3.4 3.1 + - - +
71C GLU* 3.0 41.4 + - - +
85C ARG* 3.7 24.8 - - - +
88C GLN* 3.2 15.5 + - - +
106C HIS* 3.4 41.0 + - + +
556H ASP* 3.3 41.5 + - - +
557H ASP* 2.9 35.4 + - - +
558H PTR 2.7 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C SER* 3.3 6.5 + - - +
67C ARG* 1.3 90.7 - - + +
69C GLN* 1.3 64.1 + - + +
71C GLU* 3.3 23.4 + - - +
72C ASN* 3.0 32.1 + - - +
88C GLN* 4.6 1.5 + - - -
556H ASP* 5.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 4.4 17.0 - - - +
64C GLY 4.1 3.1 - - - +
65C LEU* 3.6 25.9 - - + +
66C SER* 2.9 42.8 + - - +
68C HIS* 1.3 75.7 - - + +
70C ALA* 1.3 56.7 + - - +
72C ASN* 3.3 7.4 + - - +
73C LEU* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU* 3.9 15.8 - - + +
66C SER 2.9 17.4 + - - +
67C ARG 3.4 5.6 - - - +
69C GLN* 1.3 74.9 - - - +
71C GLU* 1.3 59.4 + - - +
73C LEU* 3.9 1.7 - - - +
74C LEU* 3.0 37.8 + - - +
83C ILE* 4.7 6.7 - - + -
85C ARG* 3.8 12.6 - - - -
97C SER* 3.8 24.7 - - - +
104C VAL* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ARG* 3.0 28.8 + - - +
68C HIS* 3.3 27.9 + - - +
70C ALA* 1.3 72.3 - - - +
72C ASN* 1.3 69.2 + - - +
74C LEU 3.4 0.5 + - - -
75C MET* 3.0 31.9 + - + +
104C VAL* 3.7 23.7 - - + +
106C HIS* 2.7 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C HIS* 3.0 24.4 + - - +
69C GLN* 3.7 6.1 - - - +
71C GLU* 1.3 80.3 - - - +
73C LEU* 1.3 67.0 + - - +
75C MET* 3.5 13.8 + - - +
76C GLY* 3.7 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN* 3.4 49.1 - - + +
75A MET* 3.8 33.7 - - + -
76A GLY 5.7 0.2 - - - +
65C LEU* 4.0 9.4 - - + -
69C GLN 2.9 17.3 + - - +
70C ALA 3.9 2.9 - - - +
72C ASN* 1.3 78.9 - - - +
74C LEU* 1.3 64.0 + - + +
76C GLY* 3.1 17.2 + - - -
77C LYS* 3.6 27.7 - - + +
83C ILE* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ALA 3.0 21.2 + - - +
73C LEU* 1.3 71.7 - - + +
75C MET* 1.3 61.0 + - - +
76C GLY 3.0 2.2 - - - -
77C LYS* 2.9 41.1 + - + +
81C PHE* 3.8 9.2 - - + +
82C PHE* 3.8 27.4 - - - +
83C ILE* 4.0 18.6 - - + +
97C SER* 3.3 44.4 - - - +
98C VAL 4.1 0.9 - - - +
99C ARG* 3.1 22.3 + - + +
104C VAL* 3.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLU* 3.0 24.3 + - + +
72C ASN* 3.9 9.2 - - - +
73C LEU 3.3 0.4 - - - -
74C LEU* 1.3 76.5 - - - +
76C GLY* 1.3 59.1 + - - +
77C LYS 3.8 0.3 - - - +
99C ARG* 2.8 52.6 + - - +
102C ASP 4.0 12.3 - - - +
103C ASP* 3.7 22.4 - - - -
104C VAL* 3.8 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASN 3.7 5.1 + - - -
73C LEU 3.1 10.1 + - - -
74C LEU 3.0 1.0 - - - -
75C MET* 1.3 78.3 - - - +
77C LYS* 1.3 60.0 + - - +
78C ASP* 5.4 0.2 - - - +
----------------------------------------------------------
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