Contacts of the helix formed by residues 122 - 134 (chain C) in PDB entry 3IFS
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 122 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C ASN* 2.9 15.0 + - - -
121C ILE* 1.3 74.1 - - - +
123C SER* 1.3 61.3 + - - +
124C THR* 3.4 3.6 + - - -
125C TYR* 3.1 26.2 + - - +
126C MSE 3.1 29.7 + - - +
274D TYR 4.7 2.0 - - - -
275D GLU* 2.5 34.7 + - - -
276D PRO* 3.8 13.5 - - - +
363D ASN* 4.8 0.4 - - - +
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Residues in contact with SER 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE 3.8 4.4 + - - -
122C SER* 1.3 70.5 - - - +
124C THR* 1.3 59.5 + - - +
126C MSE 4.5 0.4 - - - -
127C LYS* 2.9 31.7 + - - +
275D GLU* 5.2 0.6 + - - -
335D SER* 3.1 10.7 + - - -
337D HIS* 2.7 26.7 + - - +
338D GLU* 4.0 2.3 - - - -
339D LEU* 3.9 29.4 - - - +
359D VAL* 3.9 24.1 - - - +
360D ASP* 4.4 10.1 + - - +
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Residues in contact with THR 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C SER* 3.2 7.0 + - - -
123C SER* 1.3 77.1 + - - +
125C TYR* 1.3 66.0 + - - +
127C LYS* 3.9 0.5 - - - +
128C ASP* 2.9 45.6 + - - +
99D SER* 4.1 4.9 - - - +
275D GLU* 4.4 9.1 + - - -
335D SER* 3.2 10.3 + - - -
336D THR* 3.3 20.4 + - + +
337D HIS* 3.2 38.4 + - + +
389D LEU* 6.4 1.1 - - + -
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Residues in contact with TYR 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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90C ARG* 5.2 4.0 + - - -
116C PHE* 2.6 33.2 + - - +
117C VAL* 4.2 12.8 - - + -
119C GLN* 3.2 23.8 + - - -
120C ASN* 3.5 21.1 - - - +
122C SER* 3.1 25.4 + - - +
124C THR* 1.3 79.1 - - - +
126C MSE 1.3 60.3 + - + +
128C ASP* 3.3 2.3 + - - +
129C LEU* 2.9 30.4 + - + +
99D SER* 3.9 18.6 - - - +
100D PHE* 3.6 35.4 - + - -
276D PRO* 4.1 17.7 - - + -
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Residues in contact with MSE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C VAL* 4.0 17.0 - - + -
118C GLY 5.2 0.4 - - - +
120C ASN* 3.4 33.9 - - - +
121C ILE* 4.0 6.7 - - + -
122C SER 3.1 20.8 + - - +
125C TYR* 1.3 77.8 - - + +
127C LYS* 1.3 64.7 + - - +
129C LEU* 3.2 6.0 + - - +
130C MSE 3.2 25.8 + - + +
151C GLU 5.2 1.6 - - - +
154C LEU* 5.5 3.8 - - + -
155C ALA* 4.3 24.7 - - + +
158C ILE* 4.1 25.4 - - - -
159C PHE* 3.7 19.2 - - + -
339D LEU* 3.8 16.4 - - + -
359D VAL* 4.4 9.6 - - + -
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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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123C SER 2.9 19.9 + - - +
124C THR 3.9 1.3 - - - +
126C MSE 1.3 75.1 - - - +
128C ASP* 1.3 64.3 + - - +
130C MSE 3.2 38.0 + - - +
131C ASP* 3.6 12.8 + - - +
337D HIS* 3.7 37.7 - - + +
338D GLU 5.2 2.4 + - - +
339D LEU* 4.1 22.9 - - + +
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Residues in contact with ASP 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 THR* 2.9 26.6 + - - +
125C TYR 3.6 4.0 - - - +
127C LYS* 1.3 78.4 - - - +
129C LEU* 1.3 61.9 + - - +
131C ASP* 3.0 15.3 + - - +
132C VAL 3.7 1.7 + - - -
97D ASN 4.9 0.2 - - - +
98D HIS* 3.1 50.5 + - + -
99D SER* 2.5 40.3 + - - -
100D PHE* 3.9 1.5 - - + -
337D HIS* 3.2 24.3 + - - -
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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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78C LEU* 3.6 27.1 - - + -
115C LEU* 3.4 37.0 - - + -
116C PHE 4.4 4.7 - - - +
117C VAL* 3.7 26.2 - - + -
125C TYR* 2.9 16.9 + - + +
126C MSE 3.2 8.3 + - - +
128C ASP* 1.3 73.1 - - - +
130C MSE 1.3 65.2 + - - +
132C VAL* 2.8 18.3 + - + +
133C LEU* 3.1 15.3 + - + +
159C PHE* 3.9 13.9 - - + -
100D PHE* 3.5 25.3 - - + -
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Residues in contact with MSE 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 MSE 3.2 17.1 + - - +
127C LYS* 3.2 30.6 + - + +
129C LEU* 1.3 75.8 - - - +
131C ASP* 1.3 64.3 + - - +
133C LEU* 3.2 12.6 + - - +
134C GLU* 3.2 22.7 + - - +
158C ILE* 3.5 32.1 - - + -
159C PHE* 3.9 7.6 - - + -
162C LEU* 3.7 35.9 - - + -
339D LEU* 4.1 24.5 - - + -
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Residues in contact with ASP 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 LYS* 3.6 11.3 + - - +
128C ASP* 3.0 15.3 + - - +
130C MSE 1.3 80.3 - - - +
132C VAL* 1.3 59.8 + - - +
134C GLU* 3.3 15.1 - - - +
98D HIS* 2.7 33.0 + - + +
104D LEU* 4.1 8.7 - - + -
108D GLN* 3.0 28.1 + - - +
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Residues in contact with VAL 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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76C ILE* 3.8 8.4 - - + +
113C GLN* 4.6 4.9 - - - +
115C LEU* 3.7 27.6 - - + -
128C ASP 4.2 2.5 - - - +
129C LEU* 2.8 11.0 + - - +
131C ASP* 1.3 77.4 - - - +
133C LEU* 1.3 62.0 + - - +
134C GLU 3.5 1.4 + - - +
136C LYS* 3.6 18.6 - - - +
100D PHE* 3.5 41.7 - - + -
103D THR* 4.1 23.8 - - + +
104D LEU* 4.4 11.2 - - + +
108D GLN* 5.2 1.3 - - - +
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Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ILE* 3.9 29.8 - - + -
78C LEU* 4.4 7.6 - - + -
115C LEU* 4.8 0.4 - - + -
129C LEU* 3.1 21.1 + - + +
130C MSE 3.2 11.4 + - - +
132C VAL* 1.3 76.0 - - - +
134C GLU* 1.3 65.3 + - - +
135C GLY 3.3 0.7 + - - -
136C LYS* 3.0 24.5 + - - +
138C PHE* 4.0 46.2 - - + -
159C PHE* 3.8 35.2 - - + -
162C LEU* 4.6 5.4 - - + -
166C LYS* 5.1 1.9 - - - +
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Residues in contact with GLU 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 MSE 3.2 10.7 + - - +
131C ASP* 3.3 20.4 - - - +
132C VAL 3.2 2.5 - - - +
133C LEU* 1.3 75.7 - - - +
135C GLY* 1.3 68.4 + - - +
136C LYS* 3.4 9.0 + - - +
108D GLN* 4.5 8.7 + - - +
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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