Contacts of the helix formed by residues 121 - 135 (chain C) in PDB entry 4IGM
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 ALA 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C PRO* 3.5 33.0 - - + -
118C PRO* 2.9 12.5 + - + +
120C GLN* 1.3 79.4 - - - +
122C PRO* 1.3 56.5 - - - +
123C GLU 3.3 2.7 - - - -
124C LEU* 3.0 19.8 + - + +
125C ALA 2.8 29.6 + - - -
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Residues in contact with PRO 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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119C MET 3.8 7.8 - - - +
120C GLN 3.5 8.5 - - - +
121C ALA* 1.3 85.8 - - - +
123C GLU* 1.3 61.5 + - - +
125C ALA* 3.4 4.1 + - + +
126C VAL* 3.1 31.2 + - - +
150C TRP* 4.2 14.8 - - + -
156C GLU* 3.1 31.6 - - + +
157C LEU* 4.5 3.4 - - + -
159C PRO* 5.1 9.2 - - + -
160C VAL* 3.9 17.2 - - + +
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Residues in contact with GLU 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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121C ALA 3.1 1.0 + - - -
122C PRO* 1.3 77.8 - - - +
124C LEU* 1.3 67.6 + - + +
126C VAL* 3.5 6.4 + - + +
127C LYS* 3.4 34.3 + - + +
159C PRO* 6.4 0.4 - - - -
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Residues in contact with LEU 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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86C PRO* 4.0 27.6 - - + +
87C GLU* 3.4 40.8 - - - +
90C LEU* 4.2 22.2 - - + +
118C PRO* 3.9 11.3 - - + +
121C ALA* 3.0 15.9 + - + +
123C GLU* 1.3 79.5 - - + +
125C ALA* 1.3 63.4 + - - +
127C LYS* 3.3 11.6 + - + +
128C GLU* 3.0 23.0 + - - +
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Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU* 3.6 19.5 - - + +
118C PRO* 3.5 35.1 - - - +
119C MET* 4.4 6.5 - - - -
121C ALA 2.8 11.1 + - - +
122C PRO* 3.7 12.8 - - + +
123C GLU 3.3 0.2 - - - -
124C LEU* 1.3 73.2 - - - +
126C VAL* 1.3 51.8 + - - +
128C GLU 3.3 1.4 + - - -
129C MET* 2.8 35.0 + - - +
160C VAL* 4.2 12.1 - - + -
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Residues in contact with VAL 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 PRO 3.1 18.2 + - - +
123C GLU* 3.9 7.0 - - + +
125C ALA* 1.3 70.8 - - - +
127C LYS* 1.3 64.0 + - + +
129C MET* 3.2 9.1 + - - +
130C GLU* 2.8 44.7 + - - +
159C PRO* 3.8 28.0 - - + +
160C VAL* 3.9 15.0 - - + -
163C ALA* 3.7 21.8 - - + -
166C ARG* 5.7 0.4 - - - +
167C LEU* 5.4 0.3 - - - +
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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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90C LEU* 6.1 1.8 - - + -
123C GLU* 3.4 27.1 + - + +
124C LEU* 3.3 15.7 + - + +
126C VAL* 1.3 78.2 - - + +
128C GLU* 1.3 62.7 + - - +
130C GLU* 3.1 23.6 + - - +
131C ARG* 3.1 21.3 + - - +
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Residues in contact with GLU 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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90C LEU* 3.6 25.6 - - + +
93C CYS* 4.4 3.6 - - + -
94C GLN* 3.5 24.1 + - - -
97C ASN* 2.9 31.8 + - - +
116C THR 4.2 2.5 - - - +
117C LEU* 3.8 10.1 - - + -
118C PRO* 4.0 6.1 - - + -
124C LEU 3.0 10.8 + - - +
125C ALA 3.8 3.4 - - - +
127C LYS* 1.3 75.3 - - - +
129C MET* 1.3 57.6 + - - +
131C ARG* 3.1 41.5 + - - +
132C CYS* 2.9 29.6 + - - -
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Residues in contact with MET 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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117C LEU* 3.5 27.1 - - + +
125C ALA 2.8 18.5 + - - +
126C VAL* 3.6 7.9 - - - +
128C GLU* 1.3 73.3 - - - +
130C GLU* 1.3 62.2 + - - +
132C CYS* 3.7 3.9 - - - +
133C VAL* 3.0 31.0 + - + +
141C VAL* 4.6 2.7 - - + -
160C VAL* 3.3 42.8 - - + +
163C ALA* 4.2 8.1 - - + -
164C ALA* 3.7 34.8 - - + -
167C LEU* 4.2 10.1 - - + -
169C CYS* 4.0 22.4 - - - -
171C LEU* 4.9 4.7 - - + -
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Residues in contact with GLU 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 VAL* 2.8 29.5 + - - +
127C LYS* 3.1 27.8 + - - +
129C MET* 1.3 76.0 - - - +
131C ARG* 1.3 54.0 + - - +
133C VAL* 3.9 0.3 - - - +
134C LYS* 2.7 47.7 + - + +
166C ARG* 3.5 20.5 + - - -
167C LEU* 4.0 27.0 - - + +
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Residues in contact with ARG 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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94C GLN* 3.5 25.2 + - - +
97C ASN* 4.6 0.4 - - - +
98C ASN* 2.4 35.3 + - - +
127C LYS 3.1 12.2 + - - +
128C GLU* 3.1 41.8 + - - +
129C MET 3.2 0.2 - - - -
130C GLU* 1.3 76.0 - - - +
132C CYS* 1.3 58.5 + - - +
134C LYS* 5.0 0.2 - - - -
135C GLU* 2.9 62.1 + - - +
136C LEU* 3.2 37.7 + - - +
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Residues in contact with CYS 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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97C ASN* 3.2 39.5 - - - -
115C GLY* 4.4 5.6 - - - -
117C LEU* 4.6 5.8 - - - -
128C GLU* 2.9 29.0 + - - +
129C MET* 3.7 6.3 - - - +
131C ARG* 1.3 71.7 - - - +
133C VAL* 1.3 59.1 + - + +
136C LEU* 3.6 12.8 - - - +
137C GLY 3.1 9.4 + - - -
138C PHE* 2.9 46.9 + - + +
141C VAL* 4.7 8.1 - - + -
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Residues in contact with VAL 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 MET* 3.0 19.1 + - + +
130C GLU 4.1 1.8 - - - +
132C CYS* 1.3 79.3 - - + +
134C LYS* 1.3 71.9 + - + +
137C GLY* 3.6 16.5 + - - -
138C PHE* 3.8 18.2 - - + +
139C PRO* 5.8 0.7 - - + -
141C VAL* 5.9 0.2 - - + -
167C LEU* 3.8 32.8 - - + +
168C LYS 5.4 1.6 - - - +
169C CYS* 4.0 32.3 - - + -
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Residues in contact with LYS 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 GLU* 2.7 32.3 + - + +
133C VAL* 1.3 82.4 - - + +
135C GLU* 1.3 66.2 + - + +
137C GLY 4.5 0.9 + - - -
167C LEU* 3.8 27.1 - - + +
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Residues in contact with GLU 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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131C ARG* 2.9 49.1 + - + +
134C LYS* 1.3 80.9 - - + +
136C LEU* 1.3 69.0 + - + +
137C GLY* 3.3 1.8 + - - -
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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
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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