Contacts of the helix formed by residues 111 - 131 (chain C) in PDB entry 5F0P
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 111 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ARG* 3.8 14.7 + - - +
106C ASP* 3.6 19.9 - - - +
107C ASP* 3.7 12.6 + - - +
108C GLY 3.6 20.3 + - - +
109C ILE 3.4 2.0 - - - -
110C PHE* 1.3 77.4 - - - +
112C ASP* 1.3 61.8 + - - +
113C ASN* 3.4 16.6 + - - +
114C PHE* 3.5 22.3 + - + +
115C ILE* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C PHE 4.6 5.6 - - - +
111C ASP* 1.3 76.7 + - - +
113C ASN* 1.3 63.0 + - - +
115C ILE* 3.9 9.2 - - - +
116C GLU* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ASP* 3.4 12.3 + - - +
112C ASP* 1.3 80.5 + - - +
114C PHE* 1.3 65.0 + - - +
116C GLU* 3.8 6.0 - - - +
117C GLU* 3.2 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLY 5.1 2.0 - - - -
96C ALA* 3.7 11.4 - - + -
99C ARG* 3.4 36.3 - - - +
109C ILE* 3.4 51.1 - - + -
111C ASP* 3.3 23.5 + - + +
113C ASN* 1.3 76.2 - - - +
115C ILE* 1.3 63.0 + - + +
117C GLU* 3.3 6.1 + - + +
118C ARG* 2.8 77.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PRO* 3.5 36.8 - - + -
38C THR* 6.1 0.7 - - - +
47C THR* 4.4 15.5 - - + +
49C TYR* 4.0 16.4 - - + +
109C ILE 3.8 13.0 - - - +
110C PHE* 3.7 27.1 - - + +
111C ASP 2.9 21.7 + - - +
112C ASP* 4.0 9.6 - - - +
114C PHE* 1.3 78.0 - - + +
116C GLU* 1.3 55.4 + - - +
118C ARG* 3.7 5.7 - - - +
119C LYS* 2.8 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ASP 3.0 19.0 + - - +
113C ASN* 3.8 8.3 - - - +
115C ILE* 1.3 77.3 - - - +
117C GLU* 1.3 62.3 + - - +
119C LYS* 3.4 33.4 + - - +
120C GLN* 2.9 56.0 + - - +
203C SO4 4.2 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C PRO* 4.9 2.5 - - - +
113C ASN 3.2 16.3 + - - +
114C PHE* 3.9 5.5 - - + +
116C GLU* 1.3 76.4 - - - +
118C ARG* 1.3 66.9 + - - +
120C GLN* 3.5 10.4 + - + +
121C GLY* 3.1 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 5.9 3.0 - - - -
49C TYR* 3.1 30.4 + - + +
71C TYR* 3.7 38.4 - - + +
93C PRO* 3.9 14.3 - - + +
94C GLY 3.3 24.0 + - - -
96C ALA 4.1 0.4 - - - +
109C ILE* 4.4 4.9 - - - +
114C PHE* 2.8 58.3 + - + +
115C ILE* 3.7 4.0 - - - +
117C GLU* 1.3 72.4 - - - +
119C LYS* 1.3 61.7 + - - +
121C GLY* 2.9 13.5 + - - -
122C LEU* 2.9 25.4 + - + +
201C SO4 3.9 5.9 + - - -
202C SO4 2.8 35.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 3.7 27.0 + - + +
34C SER* 4.2 11.0 - - - -
36C PRO* 4.2 20.4 - - + -
49C TYR* 4.0 15.7 - - + -
115C ILE* 2.8 22.3 + - - +
116C GLU* 3.4 36.1 + - - +
118C ARG* 1.3 73.2 - - - +
120C GLN* 1.3 65.8 + - - +
122C LEU* 3.3 15.8 + - - +
123C GLU* 3.3 20.8 + - - +
203C SO4 2.8 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLU* 2.9 50.2 + - - +
117C GLU* 3.8 9.0 - - + +
119C LYS* 1.3 81.7 - - - +
121C GLY* 1.3 57.1 + - - +
123C GLU* 3.5 10.0 + - - +
124C GLN* 3.0 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C PRO 5.3 0.9 - - - +
93C PRO* 4.2 21.0 - - - +
117C GLU 3.1 10.9 + - - -
118C ARG 2.9 8.9 + - - -
120C GLN* 1.3 75.4 - - - +
122C LEU* 1.3 58.4 + - - +
124C GLN* 3.4 10.3 - - - +
125C PHE* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 3.9 12.1 - - + -
49C TYR* 3.6 40.8 - - + -
71C TYR* 3.8 27.1 - - + -
74C PHE* 3.7 47.2 - - + -
92C LEU* 4.2 1.8 - - + -
93C PRO* 4.0 9.2 - - + -
118C ARG* 2.9 22.2 + - + +
119C LYS* 3.3 8.0 + - - +
121C GLY* 1.3 73.0 - - - +
123C GLU* 1.3 55.2 + - - +
125C PHE* 3.3 5.0 + - - +
126C ILE* 2.8 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 5.8 2.1 + - - -
31C ILE 3.7 20.0 - - - +
32C ASP* 3.5 11.6 - - - +
33C VAL* 3.0 43.7 + - + +
119C LYS 3.3 9.4 + - - +
120C GLN* 3.7 12.1 - - - +
121C GLY 3.4 0.2 - - - -
122C LEU* 1.3 76.4 - - - +
124C GLN* 1.3 64.0 + - - +
126C ILE* 3.8 1.6 - - - -
127C ASN* 2.9 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLU* 5.5 0.2 - - - +
120C GLN* 3.0 21.4 + - + +
121C GLY* 3.4 13.7 - - - +
123C GLU* 1.3 77.5 - - - +
125C PHE* 1.3 62.3 + - - +
127C ASN* 4.5 1.9 - - - +
128C LYS* 3.5 52.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C PHE* 3.8 23.6 - + - -
77C LEU* 4.1 22.4 - - + -
78C ARG* 4.2 23.6 - - + -
81C LEU* 5.2 0.4 - - + -
89C VAL* 3.8 7.9 - - + -
90C PRO* 3.4 30.7 - - + -
91C PRO 3.7 17.0 - - - +
92C LEU* 3.7 24.0 - - + -
121C GLY 3.0 17.9 + - - +
122C LEU* 3.3 5.3 + - - +
124C GLN* 1.3 75.6 - - - +
126C ILE* 1.3 70.4 + - - +
128C LYS* 3.1 9.7 + - - +
129C VAL* 3.1 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ILE* 3.8 24.7 - - + -
33C VAL* 3.9 9.4 - - + -
51C ILE* 4.8 1.6 - - + -
74C PHE* 4.2 8.5 - - + -
77C LEU* 4.0 17.7 - - + -
122C LEU 2.8 23.5 + - - +
123C GLU* 3.6 13.2 - - - +
125C PHE* 1.3 78.3 - - + +
127C ASN* 1.3 60.1 + - - +
129C VAL* 4.6 2.9 - - + -
130C ALA* 2.9 34.7 + - + +
141C LEU* 4.5 8.5 - - + -
144C PHE* 3.6 29.2 - - + -
145C LEU* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLU* 4.3 16.2 - - - +
284B ARG* 4.6 1.4 + - - -
29C LEU* 4.8 4.9 - - - +
30C GLU* 4.2 4.7 - - - -
31C ILE* 3.2 47.8 + - - +
123C GLU* 2.9 30.3 + - - +
124C GLN* 4.5 2.5 - - - +
125C PHE 3.3 1.0 - - - -
126C ILE* 1.3 76.6 - - - +
128C LYS* 1.3 63.3 + - - +
130C ALA* 4.5 3.1 - - - +
131C GLY* 3.2 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLU* 3.3 32.5 - - + +
284B ARG* 2.8 32.7 + - - +
90C PRO* 3.9 32.1 - - + +
91C PRO* 5.9 2.8 - - - +
124C GLN* 3.5 41.5 + - - +
125C PHE* 3.1 9.0 + - - +
127C ASN* 1.3 77.1 - - - +
129C VAL* 1.3 63.5 + - - +
132C HIS* 3.6 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 4.7 5.4 - - + -
81C LEU* 3.5 28.5 - - + -
89C VAL* 4.1 5.2 - - + -
90C PRO* 3.7 19.5 - - + -
125C PHE* 3.1 45.5 + - + +
126C ILE* 4.1 5.4 - - + +
128C LYS* 1.3 77.3 - - - +
130C ALA* 1.3 61.3 + - - +
132C HIS* 3.3 13.2 + - - +
135C ALA* 3.4 23.2 - - + +
141C LEU* 4.0 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 3.3 11.9 - - + +
31C ILE* 3.3 26.2 - - + -
60C PHE* 4.0 4.1 - - + -
126C ILE* 2.9 21.0 + - + +
127C ASN* 4.5 1.6 - - - +
129C VAL* 1.3 76.5 - - - +
131C GLY* 1.3 56.8 + - - +
132C HIS 3.4 0.2 - - - -
136C GLN* 3.1 26.1 + - - +
141C LEU* 3.9 12.6 - - + -
145C LEU* 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 5.2 7.4 - - - +
280B ASP* 5.0 1.2 - - - +
284B ARG* 3.2 23.7 + - - -
29C LEU* 3.9 13.8 - - - +
127C ASN 3.2 13.9 + - - -
129C VAL 3.3 0.2 - - - -
130C ALA* 1.3 75.6 - - - +
132C HIS* 1.3 61.9 + - - +
133C PRO* 3.6 6.6 - - - +
136C GLN* 4.0 7.7 + - - +
----------------------------------------------------------
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