Contacts of the helix formed by residues 119 - 134 (chain C) in PDB entry 3G1Q
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 PRO 119 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ARG* 3.8 9.0 - - - +
113C GLY 5.4 0.2 - - - +
117C ALA 4.6 1.1 - - - +
118C ALA* 1.3 88.7 - - + +
120C TYR* 1.3 66.8 + - - +
121C PRO* 3.4 9.0 - - + -
122C ARG* 3.0 22.9 + - + -
123C MET 2.8 19.6 + - - -
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Residues in contact with TYR 120 (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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94C ASN* 3.7 27.6 + - + +
95C GLU* 3.5 46.7 - - + +
98C SER* 2.9 33.1 + - - -
99C PRO* 4.4 5.2 - - + -
100C ARG* 3.0 39.0 + - + +
101C GLU* 4.8 0.3 + - - -
118C ALA 4.8 0.2 - - - -
119C PRO* 1.3 70.7 - - - +
121C PRO* 1.4 73.9 - - + +
122C ARG 3.2 0.2 + - - -
123C MET* 3.2 21.2 + - + +
124C ARG* 2.9 24.5 + - - +
364C MET* 4.2 13.9 - - - +
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Residues in contact with PRO 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C GLU* 5.3 3.4 - - - +
119C PRO* 3.6 9.6 - - + -
120C TYR* 1.4 93.0 - - + +
122C ARG* 1.3 56.3 + - - +
124C ARG* 3.4 7.0 + - + +
125C GLU* 3.1 37.1 + - - +
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Residues in contact with ARG 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C GLY 5.2 2.6 + - - -
118C ALA* 4.2 5.4 - - + -
119C PRO* 3.0 30.9 + - + +
121C PRO* 1.3 78.1 - - - +
123C MET* 1.3 66.0 + - - +
125C GLU* 3.2 10.6 + - - +
126C GLN* 2.9 42.1 + - - +
270C TYR* 3.2 43.2 - - + -
272C ASP* 4.2 14.6 + - - -
274C THR* 5.0 1.4 + - - -
275C PRO 5.0 1.6 + - - -
277C SER 5.4 0.2 - - - +
280C GLU* 3.0 29.9 + - - -
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Residues in contact with MET 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ASN* 3.3 37.0 - - - +
99C PRO* 3.9 20.9 - - - -
100C ARG* 6.4 0.2 - - - -
115C ALA* 3.2 33.2 - - - +
116C TYR* 4.0 19.5 - - - +
118C ALA* 3.8 6.7 - - - +
119C PRO 2.8 12.0 + - - +
120C TYR* 3.4 26.5 - - + +
122C ARG* 1.3 77.2 - - - +
124C ARG* 1.3 77.1 + - - +
126C GLN* 3.2 5.5 + - - +
127C LEU* 3.0 34.1 + - + +
420C HIS* 3.9 4.3 - - + -
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Residues in contact with ARG 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ASN* 3.1 30.5 - - - +
120C TYR 2.9 15.9 + - - +
121C PRO* 3.7 8.3 - - + +
123C MET* 1.3 92.8 - - + +
125C GLU* 1.3 58.6 + - + +
127C LEU* 3.5 16.3 - - - +
128C ASN* 2.9 55.3 + - - +
419C VAL* 3.3 30.3 + - - +
420C HIS* 3.7 5.3 + - - -
480C HEM 3.4 18.8 + - - -
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Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PRO* 3.1 21.3 + - + +
122C ARG* 3.2 9.3 + - - +
124C ARG* 1.3 76.7 - - + +
126C GLN* 1.3 58.3 + - - +
128C ASN* 3.2 12.8 + - - +
129C PHE* 2.9 42.5 + - + -
269C VAL 4.7 0.2 - - - +
270C TYR* 3.5 29.0 - - + +
271C ARG* 2.8 50.5 + - + +
272C ASP 5.1 0.5 + - - -
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Residues in contact with GLN 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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113C GLY 4.6 6.5 + - - -
114C VAL* 3.8 7.5 - - - +
115C ALA* 2.7 34.0 + - - +
118C ALA* 4.7 1.3 - - - -
122C ARG* 2.9 34.6 + - - +
123C MET* 3.2 3.3 + - - +
125C GLU* 1.3 75.7 - - - +
127C LEU* 1.3 62.0 + - - +
129C PHE* 3.2 12.9 + - - +
130C LEU* 3.1 17.5 + - - +
270C TYR* 2.9 31.5 + - + +
276C MET* 4.5 4.9 - - - -
280C GLU* 3.6 24.9 + - - +
284C MET* 3.6 26.4 - - + +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ALA* 5.4 5.8 - - + -
116C TYR* 4.1 13.9 - - + +
123C MET* 3.0 38.8 + - + +
124C ARG* 3.5 22.9 - - - +
126C GLN* 1.3 75.0 - - + +
128C ASN* 1.3 51.8 + - - +
130C LEU* 3.2 1.3 + - - -
131C ALA* 2.7 36.0 + - - +
284C MET* 4.2 16.8 - - + -
287C ALA* 6.4 0.7 - - + -
420C HIS* 4.0 6.1 - - + +
423C ILE* 3.6 10.6 - - + +
480C HEM 3.4 56.8 - - + +
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Residues in contact with ASN 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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124C ARG* 2.9 44.8 + - - +
125C GLU* 3.4 13.0 - - - +
127C LEU* 1.3 73.4 - - - +
129C PHE* 1.3 61.7 + - + +
131C ALA* 3.2 9.5 + - - +
132C GLU* 2.9 44.4 + - - +
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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 GLU* 2.9 29.6 + - + -
126C GLN* 3.2 8.3 + - - +
128C ASN* 1.3 78.4 - - + +
130C LEU* 1.3 64.4 + - - +
132C GLU* 3.3 35.6 + - - +
133C GLU* 3.5 13.5 - - - +
265C LEU* 4.0 15.7 - - + -
268C ALA* 3.4 30.1 - - + -
269C VAL 3.4 32.8 - - - -
270C TYR* 3.7 36.8 - + - -
276C MET* 3.7 18.8 - - + -
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Residues in contact with LEU 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 GLN 3.1 7.1 + - - -
127C LEU 3.7 5.6 - - - +
129C PHE* 1.3 73.3 - - - +
131C ALA* 1.3 68.6 + - - +
133C GLU* 3.0 13.3 + - - +
134C LEU* 3.4 22.3 + - + +
261C LEU* 4.1 23.3 - - + -
265C LEU* 4.1 12.0 - - + +
284C MET* 3.9 44.4 - - + +
287C ALA* 4.8 1.1 - - + -
288C ALA* 4.0 27.4 - - + +
423C ILE* 3.9 5.8 - - + -
480C HEM 3.7 31.0 - - + -
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Residues in contact with ALA 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 LEU 2.7 21.7 + - - +
128C ASN* 3.2 11.2 + - - +
130C LEU* 1.3 74.5 - - - +
132C GLU* 1.3 61.9 + - + +
134C LEU* 3.0 15.3 + - - +
135C THR* 3.4 15.8 + - + +
423C ILE* 3.6 34.7 - - + +
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Residues in contact with GLU 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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128C ASN* 2.9 32.2 + - - +
129C PHE* 3.4 29.8 - - - +
130C LEU 3.1 0.2 - - - -
131C ALA* 1.3 77.2 - - + +
133C GLU* 1.3 65.5 + - - +
134C LEU 3.2 0.2 - - - -
135C THR* 3.0 29.6 + - + -
138C LYS* 3.3 13.9 - - - -
268C ALA* 5.6 1.6 - - - +
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Residues in contact with GLU 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 3.5 15.2 - - - +
130C LEU 3.0 7.6 + - - +
132C GLU* 1.3 83.1 - - - +
134C LEU* 1.3 65.8 + - + +
135C THR 3.5 0.4 - - - -
138C LYS* 3.8 38.2 + - - +
142C PHE* 5.2 4.0 - - - -
183C LEU* 5.1 5.5 - - - +
260C ASP 4.2 7.8 - - - +
261C LEU* 3.4 33.5 - - + +
264C GLY* 3.2 37.6 - - - +
265C LEU* 4.3 9.6 - - + -
267C SER* 5.1 0.2 + - - -
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Residues in contact with LEU 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 LEU* 3.6 37.5 - - + +
131C ALA 3.0 8.2 + - - +
133C GLU* 1.3 84.6 - - + +
135C THR* 1.3 61.9 + - - +
139C PHE* 3.5 20.3 - - - -
142C PHE* 6.1 0.4 - - + -
183C LEU* 4.1 23.3 - - + -
261C LEU* 5.5 2.0 - - + -
288C ALA* 5.6 1.3 - - + -
423C ILE* 3.8 32.5 - - + +
424C GLY* 4.3 3.8 - - - -
426C LYS* 5.1 3.3 - - - +
427C PHE* 4.6 15.4 + - + +
480C HEM 3.8 39.7 - - + -
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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
------------------------------------------------------------
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