Contacts of the helix formed by residues 110 - 131 (chain C) in PDB entry 5IWG
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 GLY 110 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C TYR* 3.2 19.8 - - - -
85C ARG* 6.3 1.0 - - - +
108C PHE 3.4 0.6 + - - -
109C ASP* 1.3 73.3 - - - +
111C LEU* 1.3 59.0 + - - +
112C PHE 3.3 2.9 - - - -
113C GLU* 3.2 18.6 + - - -
114C PHE* 2.9 26.9 + - - +
405C PEG 5.5 1.1 - - - -
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 4.4 13.9 - - + +
84C ILE* 4.1 28.3 - - + +
101C VAL* 4.8 3.4 - - + -
106C PRO 4.1 9.6 - - - +
107C VAL* 4.4 7.2 - - + -
108C PHE* 3.2 38.5 + - + +
109C ASP 3.3 0.4 + - - -
110C GLY* 1.3 75.2 - - - +
112C PHE* 1.3 63.9 + - - +
114C PHE* 3.3 5.1 + - + +
115C CYS* 3.1 30.7 + - - -
157C TYR* 3.5 57.0 - - + -
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Residues in contact with PHE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ALA* 3.9 18.4 - - + -
69C MET* 3.7 32.1 - - + -
78C ILE* 4.1 10.5 - - + -
81C LEU* 3.7 24.3 + - + +
82C ARG* 3.4 51.8 - - + +
85C ARG* 6.1 0.7 - - - +
110C GLY 3.3 0.4 - - - -
111C LEU* 1.3 80.3 - - - +
113C GLU* 1.3 68.6 + - - +
115C CYS* 3.1 10.6 + - + +
116C GLN* 2.9 55.7 + - + +
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Residues in contact with GLU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C TYR* 3.4 21.5 - - + +
63C LYS* 3.8 22.3 + - - +
110C GLY* 3.2 22.4 + - - +
112C PHE* 1.3 83.8 + - - +
114C PHE* 1.3 57.3 - - - +
116C GLN* 3.3 22.0 + - - +
117C LEU* 3.0 33.4 + - - +
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Residues in contact with PHE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ILE* 3.4 30.3 - - + -
27C TYR* 3.6 33.5 - + + -
29C TYR* 3.5 21.3 - + - -
37C PRO* 3.8 33.9 - - + -
108C PHE* 3.8 17.7 - + + -
110C GLY 2.9 13.2 + - - +
111C LEU* 3.4 11.9 - - + +
113C GLU* 1.3 76.9 - - - +
115C CYS* 1.3 63.4 + - - +
117C LEU* 3.4 3.0 + - - +
118C SER* 3.1 25.4 + - - -
144C LEU* 5.3 3.6 - - + -
157C TYR* 5.3 4.3 - + - -
403C IWX 3.0 32.8 - + - -
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Residues in contact with CYS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C MET* 3.8 7.4 - - + -
81C LEU* 4.5 6.7 - - - -
111C LEU* 3.1 30.8 + - - -
112C PHE* 3.4 11.7 - - + +
114C PHE* 1.3 78.1 - - - +
116C GLN* 1.3 60.1 + - - +
118C SER* 3.2 6.6 + - - -
119C THR* 2.8 33.0 + - - -
144C LEU* 6.2 2.2 - - - -
157C TYR* 3.7 31.6 - - - -
158C VAL* 3.7 26.5 - - + -
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Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LYS* 3.8 31.8 + - + +
64C ALA* 3.0 39.8 + - - +
65C THR* 4.3 5.9 - - - +
66C ALA 4.8 0.4 - - - +
69C MET* 3.7 10.5 - - + -
112C PHE* 2.9 48.4 + - + +
113C GLU* 3.3 26.9 + - - +
115C CYS* 1.3 76.6 - - - +
117C LEU* 1.3 56.4 + - - +
120C GLY* 2.9 23.7 + - - -
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Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ASP* 3.3 43.5 - - + +
23C ASP* 4.3 8.3 - - + +
24C ILE* 4.1 16.6 - - + +
27C TYR* 3.7 37.9 - - + +
61C PRO* 4.3 17.3 - - + +
62C HIS 5.6 0.4 - - - -
63C LYS* 4.2 27.1 - - + +
113C GLU 3.0 15.5 + - - +
114C PHE 4.0 3.4 - - - +
115C CYS 3.3 0.2 - - - -
116C GLN* 1.3 74.4 - - - +
118C SER* 1.3 65.0 + - - +
120C GLY* 3.4 1.4 + - - -
121C GLY* 3.3 19.2 + - - -
139C ASN* 5.0 1.4 + - - +
141C ALA* 5.4 1.6 - - - +
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Residues in contact with SER 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ILE* 4.5 5.2 - - - +
114C PHE* 3.1 17.9 + - - -
115C CYS* 3.2 9.9 + - - -
117C LEU* 1.3 77.7 - - - +
119C THR* 1.3 65.3 + - - +
122C SER* 3.5 4.9 + - - -
139C ASN* 2.9 26.2 + - - -
141C ALA* 3.6 35.0 - - - -
142C GLY* 4.2 0.5 - - - -
144C LEU* 4.1 22.1 - - - +
158C VAL* 5.3 1.2 + - - +
160C ASP* 4.0 3.9 - - - +
403C IWX 5.0 4.0 - - - -
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Residues in contact with THR 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 3.6 20.4 - - + -
68C GLU* 5.4 0.7 - - + -
69C MET* 4.7 2.2 - - + -
115C CYS 2.8 21.1 + - - -
118C SER* 1.3 77.9 + - - +
120C GLY* 1.3 64.0 + - - +
122C SER* 3.2 3.8 + - - -
123C VAL* 3.1 32.4 + - + +
158C VAL* 3.4 22.4 + - + +
160C ASP* 3.7 17.5 - - - +
163C LEU* 3.6 29.4 - - + -
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Residues in contact with GLY 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PRO* 3.8 7.7 - - - +
62C HIS 3.3 22.5 - - - +
64C ALA* 3.8 8.5 - - - +
116C GLN 2.9 19.1 + - - -
117C LEU 3.4 2.0 + - - -
119C THR* 1.3 72.9 - - - +
121C GLY* 1.3 55.7 + - - +
123C VAL* 4.1 3.0 - - - +
124C ALA* 2.9 32.2 + - - +
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Residues in contact with GLY 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 3.9 14.0 - - - -
61C PRO* 3.6 19.8 - - - +
117C LEU 3.3 11.0 + - - -
118C SER 3.7 0.2 + - - -
119C THR 3.3 0.4 - - - -
120C GLY* 1.3 71.9 - - - +
122C SER* 1.3 60.2 + - - +
124C ALA* 4.5 0.2 - - - -
125C GLY* 3.0 23.7 + - - -
139C ASN* 3.5 24.9 - - - +
301C LEU* 5.1 0.3 - - - +
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Residues in contact with SER 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C SER 3.5 0.5 + - - -
119C THR 3.2 7.5 + - - -
121C GLY* 1.3 73.2 - - - +
123C VAL* 1.3 61.5 + - - +
125C GLY* 3.4 2.6 + - - -
126C ALA 3.1 21.8 + - - -
139C ASN* 2.8 21.0 + - - +
160C ASP* 2.6 45.2 + - - -
164C ALA* 3.6 16.1 - - - +
301C LEU* 3.8 5.3 - - - +
303C LEU* 3.4 18.6 - - - +
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ALA* 5.5 0.2 - - + -
68C GLU* 3.6 28.0 - - + +
119C THR* 3.1 25.0 + - + +
120C GLY* 4.3 3.1 - - - +
122C SER* 1.3 73.2 - - - +
124C ALA* 1.3 61.1 + - - +
126C ALA* 3.3 7.6 + - - +
127C VAL* 3.0 33.5 + - + +
160C ASP 4.7 1.1 - - - +
163C LEU* 4.0 28.0 - - + -
164C ALA* 4.1 9.6 - - - +
167C GLU* 4.5 16.6 - - + +
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Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 3.6 28.3 + - + -
61C PRO* 4.6 6.5 - - + -
62C HIS* 5.4 3.1 - - + +
120C GLY 2.9 20.2 + - - +
121C GLY* 3.9 2.0 - - - +
123C VAL* 1.3 76.5 - - - +
125C GLY* 1.3 55.5 + - - +
127C VAL* 3.4 9.2 + - - +
128C LYS* 3.0 29.1 + - - +
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Residues in contact with GLY 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TYR* 3.7 12.5 - - - -
121C GLY 3.0 14.2 + - - -
122C SER 3.7 4.3 - - - -
123C VAL 3.3 0.2 - - - -
124C ALA* 1.3 75.7 - - - +
126C ALA* 1.3 55.3 + - - +
128C LYS* 3.3 3.5 + - - +
129C LEU* 3.0 32.1 + - - +
137C ALA* 3.6 24.9 - - - +
301C LEU* 4.0 6.1 - - - -
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C SER 3.1 13.6 + - - +
123C VAL 3.5 7.9 - - - +
125C GLY* 1.3 72.6 - - - +
127C VAL* 1.3 54.3 + - - +
129C LEU* 3.3 5.2 + - - +
130C ASN* 2.8 41.3 + - - +
164C ALA* 3.4 29.8 - - + +
167C GLU* 3.8 11.7 - - + -
168C LEU* 3.8 18.3 - - + +
301C LEU* 4.3 2.8 - - + +
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C VAL* 3.0 24.8 + - + +
124C ALA* 3.7 10.5 - - - +
126C ALA* 1.3 74.8 - - - +
128C LYS* 1.3 57.4 + - - +
130C ASN* 3.3 6.8 + - + +
131C ARG* 2.9 69.1 + - + +
167C GLU* 3.6 27.1 - - + +
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Residues in contact with LYS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LYS* 4.9 2.0 - - - +
17C CYS* 3.8 15.5 - - + -
19C TYR* 3.4 26.2 - - + +
57C GLU* 4.6 2.1 + - - -
59C TYR* 3.2 32.4 + - + -
124C ALA 3.0 7.5 + - - +
125C GLY* 3.6 8.7 - - - +
127C VAL* 1.3 77.4 - - - +
129C LEU* 1.3 58.7 + - - +
131C ARG* 3.7 4.3 + - - +
132C GLN 3.6 2.1 + - - -
133C GLN* 2.9 70.1 + - + +
134C THR* 3.5 23.2 + - + -
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLY 3.0 20.8 + - - +
126C ALA* 3.6 6.3 - - - +
128C LYS* 1.3 74.6 - - - +
130C ASN* 1.3 63.9 + - - +
132C GLN* 3.2 17.0 + - - +
134C THR* 3.6 24.4 - - + +
135C ASP 3.4 28.7 - - - +
136C MET* 4.4 0.4 - - - -
137C ALA* 4.1 4.3 - - + -
168C LEU* 4.2 18.4 - - + -
172C HIS* 4.6 7.7 + - - +
262C VAL 5.4 0.4 - - - +
299C PRO* 4.1 18.4 - - + +
300C LEU 3.8 32.5 - - - +
301C LEU* 3.9 17.3 - - + +
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Residues in contact with ASN 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ALA 2.8 23.7 + - - +
127C VAL* 3.6 5.8 - - - +
129C LEU* 1.3 73.5 - - - +
131C ARG* 1.3 61.6 + - + +
132C GLN* 3.2 9.6 + - - +
167C GLU* 2.8 44.4 + - - +
168C LEU* 3.5 7.7 - - - +
171C TYR* 3.3 52.5 - - + +
172C HIS* 3.4 27.5 - - - -
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C VAL* 2.9 44.6 + - + +
128C LYS* 4.1 2.7 - - - +
129C LEU 3.3 0.6 - - - -
130C ASN* 1.3 76.1 - - + +
132C GLN* 1.3 68.8 + - - +
133C GLN* 3.2 39.9 + - + +
171C TYR* 5.8 5.2 - - + +
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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) + - + + + + + -
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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