Contacts of the helix formed by residues 120 - 138 (chain C) in PDB entry 1GO4
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 120 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C GLY 4.7 6.7 - - - +
118C GLU 3.3 5.0 + - - -
119C LYS* 1.3 77.9 - - - +
121C GLN* 1.3 64.0 + - - +
122C LYS* 4.0 8.5 - - - +
123C ALA* 3.3 23.4 + - - +
124C ILE* 3.2 21.4 + - - +
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Residues in contact with GLN 121 (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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10C GLY 2.9 28.3 + - - +
11C ILE* 4.0 24.8 - - + +
15C GLY* 6.4 0.6 - - - -
19C ILE* 4.2 17.1 - - + +
119C LYS 3.8 0.2 + - - -
120C SER* 1.3 74.8 - - - +
122C LYS* 1.3 58.7 + - - +
123C ALA 3.4 0.2 - - - -
124C ILE* 3.5 7.6 + - + +
125C GLN* 2.9 35.5 + - + +
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Residues in contact with LYS 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C SER* 3.1 8.5 + - - +
121C GLN* 1.3 76.9 - - - +
123C ALA* 1.3 61.1 + - - +
125C GLN* 3.3 5.9 + - + +
126C ASP* 3.0 49.8 + - - +
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Residues in contact with ALA 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LYS* 4.2 19.1 - - + -
120C SER* 3.3 22.0 + - - +
122C LYS* 1.3 81.3 - - - +
124C ILE* 1.3 62.2 + - - +
126C ASP* 3.4 10.1 + - - +
127C GLU* 3.1 28.5 + - - +
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Residues in contact with ILE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 3.5 43.1 - - + -
19C ILE* 4.0 16.8 - - + -
119C LYS* 4.0 13.0 - - + +
120C SER 3.2 13.6 + - - +
121C GLN* 3.7 11.0 - - + +
122C LYS 3.2 0.4 - - - -
123C ALA* 1.3 77.9 - - - +
125C GLN* 1.3 65.0 + - - +
127C GLU* 3.0 9.0 + - - +
128C ILE* 3.0 41.3 + - + +
186C PHE* 5.4 1.1 - - + -
187C THR 3.7 17.7 - - - +
188C THR* 3.8 21.8 - - + +
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Residues in contact with GLN 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE* 3.9 23.4 - - - +
22C GLU* 4.6 9.6 + - - +
48C LYS* 5.5 1.0 - - - -
49C TYR* 3.1 32.4 + - - -
121C GLN* 2.9 23.6 + - + +
122C LYS* 3.3 6.7 + - - +
124C ILE* 1.3 77.4 - - - +
126C ASP* 1.3 59.8 + - - +
128C ILE* 3.8 20.7 - - - +
129C ARG* 2.8 46.5 + - - +
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Residues in contact with ASP 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LYS* 3.0 49.9 + - - +
123C ALA* 3.6 8.6 - - - +
125C GLN* 1.3 75.3 - - - +
127C GLU* 1.3 66.9 + - + +
129C ARG* 3.7 19.0 + - - +
130C SER* 3.1 24.4 + - - -
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Residues in contact with GLU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LYS* 2.6 30.0 + - - -
123C ALA* 3.1 13.0 + - - +
124C ILE* 3.0 8.5 + - - +
126C ASP* 1.3 77.4 - - + +
128C ILE* 1.3 64.2 + - - +
130C SER* 3.2 16.3 + - - -
131C VAL* 3.2 16.5 + - - +
185C SER 4.9 3.9 - - - +
186C PHE* 3.3 16.7 - - + -
187C THR* 2.8 34.4 + - - +
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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
----------------------------------------------------------
19C ILE* 3.4 37.2 - - + +
23C PHE* 3.7 24.2 - - + -
49C TYR* 3.5 29.2 - - + +
124C ILE* 3.0 23.1 + - + +
125C GLN* 3.8 14.8 - - - +
127C GLU* 1.3 77.3 - - - +
129C ARG* 1.3 62.3 + - - +
131C VAL* 3.1 3.5 + - - +
132C ILE* 2.9 23.4 + - + +
186C PHE* 3.7 37.9 - - + -
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Residues in contact with ARG 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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49C TYR* 3.5 34.3 - - + +
50C GLY* 2.9 37.2 - - - +
51C LEU* 4.7 3.3 - - + +
125C GLN* 2.8 36.5 + - - +
126C ASP* 3.9 18.9 + - - +
128C ILE* 1.3 77.0 - - - +
130C SER* 1.3 56.9 + - - +
132C ILE* 3.5 6.3 + - - +
133C ALA* 2.9 31.6 + - - +
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Residues in contact with SER 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 ASP 3.1 13.3 + - - -
127C GLU* 3.2 11.2 + - - -
129C ARG* 1.3 77.3 - - - +
131C VAL* 1.3 58.7 + - - +
133C ALA* 3.3 6.8 + - - +
134C GLN* 3.0 33.5 + - - +
184C ARG* 3.6 36.5 + - - -
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Residues in contact with VAL 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.8 23.8 - - + -
127C GLU 3.2 13.0 + - - +
128C ILE 3.1 7.7 + - - +
130C SER* 1.3 74.3 - - - +
132C ILE* 1.3 67.4 + - - +
134C GLN* 2.9 10.4 + - - +
135C ILE* 2.8 28.7 + - + +
183C LEU* 4.8 3.4 - - + -
184C ARG* 3.4 29.4 - - + +
185C SER 4.0 12.6 - - - +
186C PHE* 4.0 13.5 - - + -
195C SER* 3.8 22.7 - - - +
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Residues in contact with ILE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PHE* 3.5 31.9 - - + -
26C PHE* 4.9 2.0 - - + -
27C GLY* 4.1 24.5 - - - +
30C SER* 5.2 3.4 - - - +
49C TYR* 3.8 26.9 - - + -
51C LEU* 4.0 8.3 - - + -
53C LEU* 3.9 34.5 - - + -
128C ILE* 2.9 20.1 + - + +
129C ARG* 3.8 5.4 - - - +
131C VAL* 1.3 75.3 - - - +
133C ALA* 1.3 63.1 + - - +
135C ILE* 3.1 11.0 + - + +
136C THR* 3.0 23.8 + - + +
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Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.9 19.5 - - + +
129C ARG 2.9 18.0 + - - +
130C SER* 3.6 7.2 - - - +
131C VAL 3.2 0.2 - - - -
132C ILE* 1.3 76.2 - - - +
134C GLN* 1.3 57.7 + - + +
136C THR* 2.9 12.6 + - - +
137C ALA* 2.9 29.0 + - - +
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Residues in contact with GLN 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 SER 3.0 15.5 + - - +
131C VAL* 2.9 12.3 + - - +
133C ALA* 1.3 73.4 - - + +
135C ILE* 1.3 69.0 + - - +
137C ALA* 3.2 15.5 + - - +
138C THR* 3.2 17.0 + - - +
182C ARG 5.4 1.2 + - - -
183C LEU* 3.2 26.5 - - + +
184C ARG* 2.7 59.7 + - - +
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Residues in contact with ILE 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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23C PHE* 4.1 30.3 - - + -
27C GLY* 4.6 9.2 - - - +
30C SER* 4.4 14.8 - - - -
31C ILE* 4.1 14.6 - - + -
34C GLN* 3.1 14.8 + - - +
100C TRP* 4.1 18.8 - - + -
102C PHE* 4.5 15.7 - - + -
131C VAL* 2.8 20.0 + - + +
132C ILE* 3.4 17.0 - - + +
134C GLN* 1.3 77.3 - - - +
136C THR* 1.3 59.6 + - + +
138C THR* 2.7 29.4 + - - -
183C LEU* 3.5 20.4 - - + -
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Residues in contact with THR 136 (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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30C SER* 4.5 6.1 - - - +
34C GLN* 3.2 19.7 - - - +
51C LEU* 4.6 6.0 - - + +
53C LEU* 4.1 25.4 - - + -
132C ILE* 3.0 18.3 + - + +
133C ALA* 2.9 18.0 + - - +
134C GLN 3.2 0.2 - - - -
135C ILE* 1.3 77.6 - - + +
137C ALA* 1.3 60.3 + - - +
139C VAL* 3.3 28.8 + - - +
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Residues in contact with ALA 137 (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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133C ALA 2.9 16.8 + - - +
134C GLN* 3.2 10.0 + - - +
136C THR* 1.3 73.7 + - - +
138C THR* 1.3 60.6 + - - +
139C VAL* 3.0 9.3 + - - -
140C THR* 3.4 24.8 + - + +
141C PHE* 4.3 3.5 - - - -
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Residues in contact with THR 138 (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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34C GLN* 3.7 7.6 + - - -
35C ARG* 5.7 0.2 - - - -
100C TRP* 3.8 13.7 - - + -
134C GLN 3.2 16.5 + - - +
135C ILE* 2.7 21.2 + - - +
137C ALA* 1.3 77.8 - - - +
139C VAL* 1.3 63.1 + - - +
140C THR 3.2 0.8 + - - -
141C PHE* 3.3 27.3 + - + -
142C LEU* 3.1 44.8 + - + +
181C VAL* 5.0 3.4 - - + -
183C LEU* 4.6 15.0 - - + -
197C VAL* 5.2 3.8 - - + -
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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