Contacts of the helix formed by residues 121 - 135 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86E PRO* 3.9 28.7 - - + -
118E PRO* 3.1 12.9 + - + +
119E MET 4.1 0.2 - - - -
120E GLN* 1.3 79.3 - - + +
122E PRO* 1.3 70.8 - - - -
123E GLU* 2.8 5.3 + - + -
124E LEU* 2.9 27.1 + - + +
125E ALA 3.0 8.5 + - - -
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Residues in contact with PRO 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E MET 3.9 4.7 - - - +
120E GLN 3.5 11.4 - - - +
121E ALA* 1.3 81.2 - - - +
123E GLU* 1.3 52.4 + - - +
125E ALA* 3.2 3.6 + - + +
126E VAL* 2.9 40.8 + - - +
150E TRP* 4.0 17.3 - - + -
156E GLU* 3.2 36.8 - - + +
157E LEU* 4.5 2.2 - - + -
159E PRO* 4.8 11.2 - - + -
160E VAL* 4.0 18.1 - - + +
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Residues in contact with GLU 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ALA* 2.8 6.2 + - + -
122E PRO* 1.3 77.1 - - + +
124E LEU* 1.3 71.9 + - + +
126E VAL* 3.5 7.3 + - - +
127E LYS* 3.4 33.0 + - + +
159E PRO* 6.4 0.2 - - - -
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Residues in contact with LEU 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E PRO* 3.6 33.4 - - + +
87E GLU* 4.0 16.8 - - - +
90E LEU* 4.1 27.7 - - + +
118E PRO* 4.0 12.6 - - + +
121E ALA* 2.9 23.8 + - + +
123E GLU* 1.3 81.2 - - + +
125E ALA* 1.3 60.7 + - - +
126E VAL 3.2 0.4 - - - -
127E LYS* 3.2 12.0 + - + +
128E GLU* 2.9 28.2 + - - +
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Residues in contact with ALA 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E LEU* 3.8 23.8 - - + +
118E PRO* 3.5 35.6 - - - +
119E MET* 4.3 6.5 - - - -
121E ALA 3.0 8.6 + - - +
122E PRO* 3.7 9.6 - - + +
124E LEU* 1.3 76.6 - - - +
126E VAL* 1.3 62.7 + - - +
128E GLU 3.5 0.2 + - - -
129E MET* 3.1 25.1 + - - +
160E VAL* 4.4 9.0 - - + -
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Residues in contact with VAL 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E PRO 2.9 20.3 + - - +
123E GLU* 3.8 6.3 - - - +
124E LEU 3.2 0.2 - - - -
125E ALA* 1.3 77.9 - - - +
127E LYS* 1.3 64.5 + - + +
129E MET* 3.3 6.5 + - - +
130E GLU* 3.1 33.8 + - - +
159E PRO* 3.2 37.9 - - + +
160E VAL* 3.8 10.1 - - + -
163E ALA* 3.8 17.0 - - + -
166E ARG* 4.6 8.5 - - - +
167E LEU* 5.0 1.6 - - - +
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Residues in contact with LYS 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E LEU* 6.3 0.7 - - + -
123E GLU* 3.4 24.1 + - - +
124E LEU* 3.2 15.8 + - + +
126E VAL* 1.3 82.1 - - + +
128E GLU* 1.3 63.0 + - - +
130E GLU* 3.4 14.7 + - + +
131E ARG* 3.1 21.9 + - - +
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Residues in contact with GLU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E LEU* 4.1 16.1 - - + +
93E CYS* 4.5 1.8 - - + -
94E GLN* 3.3 25.4 + - - +
97E ASN* 3.2 28.1 + - - +
116E THR 4.0 9.9 - - - +
117E LEU* 4.0 6.7 - - + -
118E PRO* 4.1 6.7 - - + -
124E LEU 2.9 16.0 + - - +
125E ALA 4.0 4.0 - - - +
127E LYS* 1.3 76.4 - - - +
129E MET* 1.3 56.4 + - - +
131E ARG* 2.9 48.2 + - - +
132E CYS* 2.9 25.7 + - - -
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Residues in contact with MET 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E LEU* 3.8 22.6 - - + +
125E ALA 3.1 14.9 + - - +
126E VAL* 3.6 5.2 - - - +
127E LYS 3.1 0.2 - - - -
128E GLU* 1.3 73.4 - - - +
130E GLU* 1.3 58.2 + - - +
131E ARG 3.1 1.3 - - - -
132E CYS* 2.9 4.5 + - - +
133E VAL* 2.8 37.0 + - + +
141E VAL* 4.3 7.2 - - + -
160E VAL* 3.5 44.6 - - + +
163E ALA* 4.3 6.3 - - + -
164E ALA* 3.7 30.1 - - + +
167E LEU* 3.9 12.3 - - + -
169E CYS* 3.7 28.7 - - - -
171E LEU* 5.3 0.4 - - + -
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Residues in contact with GLU 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E VAL* 3.1 21.8 + - - +
127E LYS* 3.4 20.3 - - + +
129E MET* 1.3 77.7 - - - +
131E ARG* 1.3 55.5 + - - +
133E VAL 3.7 0.2 + - - -
134E LYS* 3.1 39.2 + - + +
166E ARG* 5.0 9.3 + - - -
167E LEU* 3.7 34.8 - - + +
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Residues in contact with ARG 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E GLN* 3.5 27.8 + - - +
97E ASN* 4.4 0.6 - - - +
98E ASN* 2.4 36.5 + - - +
127E LYS 3.1 10.9 + - - +
128E GLU* 2.9 42.6 + - - +
129E MET 3.1 0.4 - - - -
130E GLU* 1.3 75.6 - - - +
132E CYS* 1.3 62.6 + - - +
135E GLU* 3.1 53.3 + - - +
136E LEU* 3.3 33.7 + - - +
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Residues in contact with CYS 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ASN* 3.3 37.7 - - - -
115E GLY* 4.1 7.6 - - - -
117E LEU* 4.6 2.0 - - - -
128E GLU* 2.9 22.9 + - - +
129E MET* 2.9 14.1 + - - +
131E ARG* 1.3 72.1 - - - +
133E VAL* 1.3 54.2 + - + +
136E LEU* 3.5 11.4 - - - +
137E GLY 3.1 9.2 + - - -
138E PHE* 2.8 51.0 + - + +
141E VAL* 4.6 13.5 - - + -
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Residues in contact with VAL 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E MET* 2.8 19.5 + - + +
130E GLU 4.1 3.4 - - - +
132E CYS* 1.3 79.2 - - + +
134E LYS* 1.3 85.1 + - + +
135E GLU 3.8 0.2 - - - -
137E GLY* 3.4 19.8 - - - -
138E PHE 3.7 15.3 - - - +
167E LEU* 4.0 25.1 - - + +
169E CYS* 3.8 36.8 - - + -
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Residues in contact with LYS 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLU* 3.1 23.6 + - + +
133E VAL* 1.3 99.6 - - + +
135E GLU* 1.3 62.7 + - + +
137E GLY* 4.6 0.7 - - - -
167E LEU* 4.2 23.0 - - + +
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Residues in contact with GLU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E ARG* 3.1 47.3 + - + +
134E LYS* 1.3 79.8 - - + +
136E LEU* 1.3 74.2 + - + +
137E GLY 3.3 1.3 + - - -
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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