Contacts of the helix formed by residues 87 - 105 (chain C) 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 ASP 87 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 4.9 6.0 - - + +
57C LEU 3.6 9.6 - - - +
58C ASN* 3.3 30.0 - - - +
59C SER 4.1 0.5 + - - -
85C THR* 3.2 6.4 - - + +
86C ARG* 1.3 80.6 - - - +
88C LYS* 1.3 58.7 + - - +
89C SER* 2.5 41.2 + - - -
90C PHE* 3.2 22.7 - - + +
91C LEU 2.9 24.4 + - - -
132C LEU* 3.7 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ARG 3.9 2.4 + - - -
87C ASP* 1.3 73.0 + - - +
89C SER* 1.3 67.0 + - - +
91C LEU* 3.4 2.0 + - - +
92C ALA* 2.9 33.8 + - + +
131C ASP* 3.5 30.8 + - + +
132C LEU* 3.4 15.4 - - + +
135C VAL* 3.6 16.5 - - + +
280D GLU* 2.7 47.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASN* 5.8 0.2 - - - -
59C SER* 2.9 28.3 + - - -
87C ASP* 2.5 22.2 + - - -
88C LYS* 1.3 82.8 + - - +
90C PHE* 1.3 62.8 + - - -
92C ALA* 3.4 5.5 + - - +
93C MET* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 3.6 26.9 - - + -
38C VAL* 4.5 3.8 - - + -
40C SER* 3.5 32.1 - - - -
57C LEU* 3.9 33.0 - - + -
58C ASN 4.2 6.5 - - - -
59C SER* 4.3 7.2 - - - +
62C LEU* 3.4 38.8 - - + +
85C THR* 3.3 29.4 - - + -
87C ASP* 3.0 24.9 + - + +
89C SER* 1.3 79.5 - - - +
91C LEU* 1.3 62.5 + - - +
93C MET* 3.3 4.0 + - - +
94C VAL* 3.0 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C THR* 5.6 5.2 - - - +
83C GLY 5.5 0.4 - - - +
85C THR* 4.6 9.4 - - + +
87C ASP 2.9 12.1 + - - +
88C LYS 3.7 6.7 - - - +
90C PHE* 1.3 80.1 - - - +
92C ALA* 1.3 63.9 + - - +
94C VAL* 3.0 31.6 + - + +
95C VAL* 3.3 5.9 + - - +
110C TYR* 5.5 1.8 - - - +
132C LEU* 3.7 13.5 - - + -
135C VAL* 3.6 18.8 - - + -
136C TYR* 3.3 63.3 - - + +
140C VAL* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LYS* 2.9 22.7 + - + +
89C SER* 3.7 6.7 - - - +
91C LEU* 1.3 74.7 - - - +
93C MET* 1.3 63.6 + - - +
95C VAL* 2.9 23.2 + - - +
96C ASP* 3.3 11.0 + - - +
135C VAL* 4.0 15.6 - - + +
139C LYS* 3.9 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C SER* 3.1 36.8 - - - +
62C LEU* 3.8 15.7 - - + -
63C GLN* 2.6 45.5 - - + +
89C SER 3.1 15.1 + - - +
90C PHE* 3.5 4.9 - - - +
92C ALA* 1.3 78.7 - - - +
94C VAL* 1.3 63.5 + - - +
96C ASP* 3.0 17.4 + - + +
97C ILE* 2.9 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 4.1 17.5 - - + -
62C LEU* 3.9 15.3 - - + -
82C THR* 3.7 30.5 - - + -
85C THR* 5.7 0.7 - - - +
90C PHE* 3.0 38.1 + - + +
91C LEU* 3.0 17.9 + - + +
93C MET* 1.3 74.9 - - - +
95C VAL* 1.3 53.6 + - + +
97C ILE* 3.2 12.4 - - + +
98C VAL* 2.7 46.9 + - + +
110C TYR* 4.7 4.9 - - + +
140C VAL* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LEU 3.6 5.4 - - - +
92C ALA* 2.9 15.3 + - - +
94C VAL* 1.3 74.7 - - + +
96C ASP* 1.3 71.6 + - - +
98C VAL* 2.8 20.5 + - - +
99C GLN* 2.8 32.5 + - - +
110C TYR* 6.0 0.7 - - + -
139C LYS* 3.6 37.7 - - + +
140C VAL* 3.6 34.5 - - + -
143C VAL* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ALA 3.4 6.5 - - - +
93C MET* 3.0 17.0 + - + +
95C VAL* 1.3 74.8 - - - +
97C ILE* 1.3 65.4 + - + +
99C GLN* 3.1 12.8 + - - +
100C GLU* 2.9 23.5 + - - +
139C LYS* 3.1 26.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 4.7 9.0 - - + -
10C ILE* 5.3 7.0 - - + -
62C LEU* 3.9 34.5 - - + -
66C TYR* 3.5 55.9 - - + -
93C MET* 2.9 28.0 + - + +
94C VAL* 3.2 10.3 - - + +
96C ASP* 1.3 75.4 - - + +
98C VAL* 1.3 66.1 + - + +
100C GLU* 3.1 9.4 + - - +
101C LEU* 3.0 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C VAL* 4.3 15.7 - - + -
94C VAL* 2.7 47.4 + - + +
95C VAL* 2.8 9.5 + - - +
97C ILE* 1.3 71.6 - - + +
99C GLN* 1.3 59.8 + - - +
101C LEU* 3.1 13.3 + - - +
102C LYS* 2.8 33.4 + - + +
108C LEU* 4.9 4.0 - - + -
110C TYR* 3.6 46.4 - - + -
143C VAL* 4.4 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 2.8 32.4 + - - +
96C ASP* 3.5 14.2 - - - +
98C VAL* 1.3 73.7 - - - +
100C GLU* 1.3 66.6 + - - +
102C LYS* 3.0 11.9 + - + +
103C GLN* 3.0 34.1 + - - +
139C LYS* 5.6 0.5 + - - -
143C VAL* 4.0 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C TYR* 3.4 31.3 + - - +
70C LYS* 3.8 18.4 + - - +
96C ASP 2.9 13.3 + - - +
97C ILE* 3.6 9.1 - - - +
99C GLN* 1.3 76.8 - - - +
101C LEU* 1.3 58.8 + - - +
103C GLN* 3.4 8.5 - - + +
104C GLN* 3.0 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 4.2 6.7 - - + -
66C TYR* 3.2 22.4 - - + +
75C ASN* 3.4 27.6 - - + +
76C GLN* 4.9 2.0 - - - -
77C TYR* 3.9 22.9 - - + +
80C VAL* 4.1 20.9 - - + -
97C ILE* 3.0 31.8 + - + +
98C VAL* 3.4 7.4 - - - +
100C GLU* 1.3 74.2 - - - +
102C LYS* 1.3 59.9 + - - +
103C GLN 3.1 1.8 - - - -
104C GLN* 3.1 12.8 + - - +
105C ASN* 2.8 31.4 + - - +
108C LEU* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C VAL* 2.8 20.2 + - + +
99C GLN* 3.0 9.8 + - + +
101C LEU* 1.3 71.8 - - - +
103C GLN* 1.3 66.5 + - - +
105C ASN 2.9 27.2 - - - +
106C PRO* 3.1 13.0 + - + +
108C LEU* 3.0 40.8 + - + +
110C TYR* 4.4 4.5 - - - -
143C VAL* 3.7 36.6 - - + -
145C ASP* 2.4 37.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLN* 3.0 23.5 + - - +
100C GLU* 3.4 12.8 - - - +
101C LEU 3.1 0.2 - - - -
102C LYS* 1.3 87.3 - - - +
104C GLN* 1.3 68.6 + - + +
105C ASN 3.4 0.2 + - - -
106C PRO* 3.9 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LYS* 3.7 7.5 + - - -
75C ASN* 3.2 43.8 + - - +
76C GLN* 4.6 10.1 - - - +
100C GLU* 3.0 33.8 - - + +
101C LEU* 3.5 12.0 - - - +
103C GLN* 1.3 78.7 - - + +
105C ASN* 1.3 60.6 + - + +
106C PRO* 3.5 5.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C TYR 3.2 25.4 - - - +
78C ASP* 4.1 10.2 - - - +
101C LEU 2.8 14.4 + - - +
102C LYS* 2.9 13.4 - - - +
104C GLN* 1.3 74.6 - - + +
106C PRO* 1.3 66.2 - - - +
107C ARG* 2.7 29.7 - - - +
108C LEU* 3.2 31.1 + - + +
----------------------------------------------------------
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