Contacts of the helix formed by residues 121 - 135 (chain C) in PDB entry 3IZ0
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 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A ARG* 6.2 1.1 - - - +
415A GLU* 4.0 32.0 + - - +
119C ALA 3.6 1.4 + - - -
120C PRO* 1.3 76.5 - - - +
122C VAL* 1.3 64.1 + - - +
123C LYS* 3.5 9.6 + - - +
124C ASP* 2.9 34.9 + - - +
125C PHE* 2.9 21.1 + - - +
172C VAL* 4.6 0.7 - - - -
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Residues in contact with VAL 122 (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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409A VAL* 6.1 5.4 - - + -
120C PRO 4.0 0.4 + - - -
121C SER* 1.3 72.0 - - - +
123C LYS* 1.3 62.4 + - - +
125C PHE* 3.3 2.5 + - + +
126C LEU* 2.9 36.3 + - + +
147C PHE* 3.6 29.8 - - + -
169C MET 3.6 13.2 - - - +
170C TYR* 3.6 26.0 - - - +
171C THR* 4.9 0.4 - - - -
172C VAL* 3.8 19.7 - - + +
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Residues in contact with LYS 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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414A GLU* 5.5 17.3 - - + -
121C SER* 3.2 9.5 - - - +
122C VAL* 1.3 79.8 - - - +
124C ASP* 1.3 65.4 + - - +
126C LEU* 3.5 7.6 + - - +
127C LYS* 3.3 55.0 + - - +
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Residues in contact with ASP 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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415A GLU* 5.4 4.2 - - - +
108C TYR* 4.3 0.6 + - - -
116C SER* 5.1 4.5 - - - +
120C PRO* 4.1 11.4 - - + +
121C SER* 2.9 32.0 + - - +
123C LYS* 1.3 76.6 - - - +
125C PHE* 1.3 67.5 + - - +
127C LYS* 2.9 20.7 + - - +
128C ILE* 2.9 31.5 + - + +
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Residues in contact with PHE 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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120C PRO* 4.5 7.1 - - + +
121C SER 2.9 11.8 + - - +
122C VAL* 3.5 7.0 - - - +
124C ASP* 1.3 76.5 - - - +
126C LEU* 1.3 74.8 + - + +
128C ILE* 3.1 8.7 + - - -
129C PHE* 2.7 40.7 + + + +
147C PHE* 5.4 1.8 - + - -
151C VAL* 4.0 28.0 - - + -
155C PHE* 5.3 2.0 - + - -
169C MET* 4.4 9.4 - - + -
172C VAL* 3.7 33.9 - - + -
178C TRP* 4.6 4.5 - + - -
181C ILE* 3.4 32.3 - - + -
185C LEU* 3.7 32.8 - - + -
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Residues in contact with LEU 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 VAL* 2.9 36.3 + - + +
123C LYS* 3.9 7.6 - - - +
124C ASP 3.1 0.2 - - - -
125C PHE* 1.3 92.0 - - + +
127C LYS* 1.3 58.5 + - - +
129C PHE* 4.1 3.2 - - + +
130C THR* 2.7 37.7 + - - -
142C LEU* 3.7 28.5 - - + -
147C PHE* 3.6 41.3 - - + -
151C VAL* 4.1 6.5 - - + -
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Residues in contact with LYS 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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108C TYR* 3.1 17.9 - - + +
110C HIS* 3.5 37.8 + - + +
123C LYS* 3.3 49.0 + - + +
124C ASP* 2.9 17.5 + - - +
126C LEU* 1.3 75.8 - - - +
128C ILE* 1.3 58.2 + - - +
130C THR* 3.8 4.3 - - - -
131C PHE* 3.0 27.5 + - - +
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Residues in contact with ILE 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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99C LEU* 4.1 14.1 - - + -
103C LEU* 3.9 13.7 - - + -
108C TYR* 3.5 25.8 - - + +
112C VAL* 5.0 4.0 - - + -
117C LEU* 3.8 28.9 - - + -
120C PRO* 5.3 4.3 - - + -
124C ASP* 2.9 24.8 + - + +
125C PHE* 3.5 9.2 - - - +
127C LYS* 1.3 74.6 - - - +
129C PHE* 1.3 64.5 + - - +
131C PHE* 3.2 2.6 + - - +
132C LEU* 3.0 34.7 + - + +
178C TRP* 5.7 2.0 - - + -
185C LEU* 3.8 26.9 - - + -
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Residues in contact with PHE 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 PHE* 2.7 33.7 + + + +
126C LEU* 4.1 4.3 - - - +
128C ILE* 1.3 75.1 - - - +
130C THR* 1.3 66.9 + - - +
132C LEU* 3.3 3.1 + - - +
133C TYR* 2.9 40.1 + + + +
140C TYR* 4.3 16.4 - + - -
142C LEU* 4.7 7.2 - - + -
151C VAL* 3.9 29.6 - - + -
154C ILE* 3.9 37.9 - - + -
155C PHE* 3.6 32.8 - + - -
158C LEU* 6.2 0.2 - - + -
185C LEU* 4.5 8.5 - - + +
188C LEU* 4.3 17.5 - - + -
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Residues in contact with THR 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 LEU 2.7 23.4 + - - -
127C LYS* 3.8 5.8 - - - -
129C PHE* 1.3 81.6 - - - +
131C PHE* 1.3 63.1 + - - +
133C TYR* 4.0 3.0 - - - +
134C GLY* 3.1 20.1 + - - -
140C TYR* 3.4 33.6 - - + +
141C GLU* 4.4 6.7 - - + -
142C LEU* 3.6 27.6 - - + +
26F ALA* 5.5 4.7 - - + -
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Residues in contact with PHE 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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102C PHE* 4.6 3.1 - + - -
103C LEU* 3.5 31.0 - - + -
106C ASN* 3.4 32.3 - - + -
107C GLY 4.6 2.5 - - - -
108C TYR* 3.4 37.7 - + + -
109C ALA 5.2 1.1 - - - -
127C LYS 3.0 18.3 + - - +
128C ILE 3.5 4.0 - - - +
129C PHE 3.2 0.2 - - - -
130C THR* 1.3 78.0 - - - +
132C LEU* 1.3 65.7 + - + +
134C GLY* 3.1 13.6 + - - -
135C PHE* 3.3 41.0 - + - -
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Residues in contact with LEU 132 (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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99C LEU* 4.1 11.4 - - + -
102C PHE* 3.5 37.7 - - + -
103C LEU* 4.2 13.2 - - + -
128C ILE* 3.0 30.5 + - + +
129C PHE 3.8 1.1 - - - +
131C PHE* 1.3 78.2 - - + +
133C TYR* 1.3 63.1 + - - +
135C PHE* 3.1 24.5 + - - +
136C LEU* 4.2 1.0 + - - +
185C LEU* 4.0 39.9 - - + +
188C LEU* 3.7 16.4 - - + -
189C ILE* 4.0 10.5 - - + -
192C ILE* 3.4 13.4 - - + +
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Residues in contact with TYR 133 (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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129C PHE* 2.9 31.7 + + + +
130C THR 4.2 2.5 - - - +
132C LEU* 1.3 77.9 - - - +
134C GLY* 1.3 53.2 + - - +
136C LEU* 2.8 39.9 + - + +
137C CYS* 2.8 25.5 + - - -
140C TYR* 3.5 43.7 - + + -
154C ILE* 3.4 45.9 - - + +
158C LEU* 4.2 14.1 - - + -
188C LEU* 4.3 7.8 - - + +
110D LEU* 3.2 34.2 - - + +
111D CYS* 5.9 0.9 - - - +
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Residues in contact with GLY 134 (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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130C THR 3.1 14.7 + - - -
131C PHE 3.1 8.4 + - - -
133C TYR* 1.3 75.1 - - - +
135C PHE* 1.3 62.4 + - - +
136C LEU 3.1 1.1 + - - -
137C CYS 3.3 14.3 - - - +
138C PRO* 3.4 24.2 - - - +
139C SER 4.5 1.6 + - - -
140C TYR* 4.5 7.8 - - - +
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Residues in contact with PHE 135 (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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102C PHE* 4.0 9.4 - + - -
106C ASN* 3.8 40.6 - - + -
131C PHE* 3.3 46.4 - + - -
132C LEU* 3.1 16.0 + - - +
133C TYR 3.1 0.6 - - - -
134C GLY* 1.3 77.3 - - - +
136C LEU* 1.3 63.1 + - - +
138C PRO* 5.2 2.6 - - - +
192C ILE* 3.9 33.7 - - + +
195C HIS* 4.9 5.4 - - - -
196C THR* 5.8 1.3 - - - -
199C LYS* 5.8 1.7 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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