Contacts of the helix formed by residues 120 - 129 (chain C) in PDB entry 3G3B
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 ILE 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C LYS 3.5 23.1 - - - +
91C SER* 3.8 13.0 - - - -
113C TRP* 4.1 10.8 - - + -
114C ASP 3.4 21.9 + - - +
115C CYS* 4.1 14.4 - - - +
117C CYS* 3.0 14.4 + - - +
119C ASP* 1.3 78.8 - - - +
121C LEU* 1.3 58.6 + - - +
122C TYR 3.4 0.4 - - - -
123C LEU* 3.0 27.9 + - + +
124C SER* 2.9 26.3 + - - -
154C VAL* 3.9 14.1 - - + -
157C VAL* 3.7 31.4 - - + -
162C THR* 4.4 2.9 - - + -
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Residues in contact with LEU 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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118C SER* 3.5 22.7 - - - +
119C ASP 3.2 2.6 - - - -
120C ILE* 1.3 75.9 - - - +
122C TYR* 1.3 62.4 + - - +
124C SER* 3.8 14.5 - - - +
125C ARG* 3.0 38.9 + - + +
157C VAL* 4.3 4.9 - - + +
158C THR 4.1 11.4 - - - +
159C LYS* 3.9 43.7 - - + -
162C THR* 4.0 21.3 - - + +
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Residues in contact with TYR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ILE* 3.8 30.1 - - + +
93C PRO 3.6 16.4 - - - -
94C ARG* 4.1 21.3 - - + +
95C GLY* 3.1 30.3 - - - -
96C ALA 3.9 2.2 - - - -
97C PHE* 3.3 26.4 + + - +
98C ASP* 3.0 22.5 + - - -
119C ASP 4.0 4.9 + - - +
120C ILE 3.4 1.2 - - - -
121C LEU* 1.3 77.9 - - - +
123C LEU* 1.3 59.7 + - - +
125C ARG* 3.8 6.7 - - + +
126C TRP* 2.8 50.0 + + + +
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Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ILE* 3.7 25.8 + - + +
97C PHE* 4.2 14.1 - - + -
108C LEU* 3.9 15.7 - - + -
113C TRP* 3.5 48.5 - - + -
119C ASP 5.0 0.2 + - - -
120C ILE* 3.0 20.1 + - + +
122C TYR* 1.3 80.9 - - - +
124C SER* 1.3 66.3 + - - +
126C TRP* 4.3 4.0 - - + -
127C ILE* 3.0 56.4 + - + +
145C ALA* 5.4 0.2 - - + -
154C VAL* 4.0 7.4 - - + -
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Residues in contact with SER 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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120C ILE 2.9 18.0 + - - -
121C LEU* 3.8 12.7 + - - +
123C LEU* 1.3 76.9 - - - +
125C ARG* 1.3 64.9 + - - +
128C SER* 3.4 24.1 + - - -
154C VAL* 3.3 33.9 + - - +
155C ARG* 3.6 7.6 + - - +
157C VAL* 3.1 30.9 + - - +
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Residues in contact with ARG 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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121C LEU* 3.0 32.7 + - + +
122C TYR* 3.8 6.3 - - + +
124C SER* 1.3 76.8 + - - +
126C TRP* 1.3 65.6 + - - +
128C SER* 3.3 6.9 + - - -
129C GLN* 3.0 55.8 + - - +
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Residues in contact with TRP 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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97C PHE* 3.5 46.5 + + + +
98C ASP* 4.9 3.6 - - - +
103C LEU* 3.8 26.0 - - + -
106C ILE* 3.9 24.0 - - + -
108C LEU* 4.7 1.8 - - + -
122C TYR* 2.8 48.0 + + + +
123C LEU* 3.3 7.6 + - + +
125C ARG* 1.3 72.8 - - - +
127C ILE* 1.3 72.4 + - + +
129C GLN* 3.4 8.6 + - - -
130C HIS* 2.6 57.1 + + + -
133C LEU* 3.8 25.8 - - + -
134C VAL* 4.2 13.0 - - + -
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Residues in contact with ILE 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 LEU* 4.2 4.5 - - + -
123C LEU* 3.0 48.1 + - + +
124C SER 4.2 0.2 - - - +
126C TRP* 1.3 83.4 - - + +
128C SER* 1.3 61.5 + - - +
130C HIS 2.9 28.6 + - - -
131C PRO* 3.5 4.5 - - - +
134C VAL* 4.1 20.4 - - + -
142C HIS* 3.8 23.8 + - + +
145C ALA* 3.9 25.8 - - + -
154C VAL* 4.1 12.6 - - + -
155C ARG* 3.6 23.3 - - + +
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Residues in contact with SER 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 SER 3.4 10.5 + - - -
125C ARG* 3.3 7.8 + - - -
127C ILE* 1.3 80.8 - - - +
129C GLN* 1.3 60.1 + - - -
130C HIS 3.6 0.3 + - - -
131C PRO* 3.8 11.2 - - - +
142C HIS* 5.9 1.1 - - - -
155C ARG* 3.1 36.1 + - - +
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Residues in contact with GLN 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 ARG* 3.0 56.4 + - - +
126C TRP* 4.0 7.1 - - - -
127C ILE 3.2 0.2 - - - -
128C SER* 1.3 78.4 - - - +
130C HIS* 1.3 83.0 + - + +
131C PRO* 3.4 4.3 - - - +
132C TRP* 3.4 18.0 - - - -
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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