Contacts of the helix formed by residues 121 - 135 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B PRO* 3.7 31.6 - - + -
118B PRO* 3.1 12.3 + - + +
119B MET 3.0 1.4 - - - -
120B GLN* 1.3 80.8 - - + +
122B PRO* 1.3 58.1 - - - +
123B GLU* 3.3 2.5 - - + -
124B LEU* 3.1 19.6 + - + +
125B ALA 2.8 30.3 + - - -
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Residues in contact with PRO 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B MET 4.0 4.7 - - - +
120B GLN 3.5 7.9 - - - +
121B ALA* 1.3 88.4 - - - +
123B GLU* 1.3 57.5 + - - +
125B ALA* 3.1 5.1 + - + +
126B VAL* 2.9 34.0 + - - +
150B TRP* 4.3 16.4 - - + -
156B GLU* 3.2 35.2 - - + +
157B LEU* 4.5 2.5 - - + -
159B PRO* 4.8 9.4 - - + -
160B VAL* 3.7 14.9 - - + +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ALA* 3.3 1.4 - - + -
122B PRO* 1.3 75.7 - - - +
124B LEU* 1.3 85.1 + - + +
126B VAL* 3.6 8.6 + - - +
127B LYS* 3.2 27.4 + - - +
159B PRO* 6.2 1.1 - - - -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PRO* 4.0 22.9 - - + +
87B GLU* 3.3 34.1 - - - +
90B LEU* 4.3 21.1 - - + +
118B PRO* 3.8 13.0 - - + +
121B ALA* 3.1 25.2 + - + +
123B GLU* 1.3 94.6 - - + +
125B ALA* 1.3 57.9 + - - +
127B LYS* 3.5 9.7 + - + +
128B GLU* 3.1 28.8 + - - +
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 3.8 20.8 - - + +
118B PRO* 3.7 22.4 - - - +
119B MET* 4.5 5.2 - - - -
121B ALA 2.8 13.6 + - - +
122B PRO* 3.1 10.7 + - + +
124B LEU* 1.3 74.9 - - - +
126B VAL* 1.3 64.5 + - - +
128B GLU 3.3 1.4 + - - -
129B MET* 2.9 25.4 + - - +
160B VAL* 3.8 18.8 - - + -
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PRO 2.9 18.5 + - - +
123B GLU* 3.8 9.2 - - - +
124B LEU 3.4 0.2 - - - -
125B ALA* 1.3 74.6 - - - +
127B LYS* 1.3 54.8 + - + +
129B MET* 2.9 9.4 + - - +
130B GLU* 2.8 56.7 + - - +
159B PRO* 3.6 36.8 - - + +
160B VAL* 4.2 4.2 - - - +
163B ALA* 4.0 17.7 - - + -
166B ARG* 5.2 1.6 - - - +
167B LEU* 5.1 0.3 - - - +
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ARG* 5.1 11.1 - - - +
90B LEU* 6.2 2.7 - - + -
123B GLU* 3.2 16.7 + - - +
124B LEU* 3.8 10.5 - - + +
125B ALA 3.2 0.4 - - - -
126B VAL* 1.3 80.8 - - + +
128B GLU* 1.3 61.0 + - - +
130B GLU* 3.4 17.3 + - - +
131B ARG* 3.1 23.0 + - - +
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 3.8 18.9 - - + +
93B CYS* 3.8 7.5 - - + +
94B GLN* 3.5 21.2 + - - +
97B ASN* 2.8 31.0 + - - +
116B THR 4.0 3.6 - - - +
117B LEU* 4.0 9.6 - - + -
118B PRO* 4.0 9.9 - - + -
124B LEU 3.1 17.6 + - - +
125B ALA 3.3 2.9 + - - +
127B LYS* 1.3 76.3 - - - +
129B MET* 1.3 57.9 + - - +
131B ARG* 3.2 37.4 + - - +
132B CYS* 3.0 26.4 + - - -
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Residues in contact with MET 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 3.8 22.2 - - + -
125B ALA 2.9 14.6 + - - +
126B VAL* 2.9 5.9 + - - +
128B GLU* 1.3 77.3 - - - +
130B GLU* 1.3 65.5 + - - +
131B ARG 3.1 1.3 - - - -
132B CYS* 3.3 3.7 + - - +
133B VAL* 3.1 24.4 + - - +
141B VAL* 4.3 5.6 - - + -
160B VAL* 3.3 45.5 - - + +
163B ALA* 4.2 4.5 - - + -
164B ALA* 3.7 21.8 - - + +
167B LEU* 3.6 22.4 - - + -
169B CYS* 3.7 25.8 - - - -
171B LEU* 5.1 2.7 - - + -
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B VAL* 2.8 26.8 + - + +
127B LYS* 3.6 27.7 - - - +
129B MET* 1.3 75.5 - - - +
131B ARG* 1.3 64.8 + - - +
134B LYS* 2.9 36.7 + - + +
166B ARG* 3.3 20.6 + - - +
167B LEU* 3.9 30.1 - - + -
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL 4.4 0.2 + - - -
106A SER* 3.5 26.4 + - - +
94B GLN* 4.0 20.0 + - - +
97B ASN* 4.4 0.6 - - - +
98B ASN* 2.4 40.5 + - - +
127B LYS 3.1 15.0 + - - +
128B GLU* 3.2 38.7 + - - +
130B GLU* 1.3 80.5 - - - +
132B CYS* 1.3 57.2 + - - +
135B GLU* 2.9 61.1 + - + +
136B LEU* 3.1 29.0 + - - +
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Residues in contact with CYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ASN* 3.3 37.0 - - - -
115B GLY* 4.2 6.5 - - - -
117B LEU* 4.7 1.8 - - - -
128B GLU* 3.0 27.7 + - - +
129B MET* 3.3 7.8 + - - +
131B ARG* 1.3 76.6 - - - +
133B VAL* 1.3 57.3 + - + +
136B LEU* 3.5 12.5 - - - +
137B GLY 3.1 8.7 + - - -
138B PHE* 2.9 46.8 + - + +
141B VAL* 4.6 13.0 - - + -
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B MET* 3.1 17.3 + - + +
130B GLU 4.1 1.3 - - - +
132B CYS* 1.3 80.4 - - + +
134B LYS* 1.3 77.1 + - + +
137B GLY* 3.4 18.4 + - - -
138B PHE* 3.8 21.0 - - + +
139B PRO 5.4 0.2 - - - -
140B GLY* 5.4 0.4 - - - +
167B LEU* 3.8 31.6 - - + +
168B LYS 5.8 0.2 - - - +
169B CYS* 4.0 33.9 - - + -
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 2.9 28.0 + - + +
133B VAL* 1.3 82.9 - - + +
135B GLU* 1.3 66.5 + - + +
137B GLY 4.7 1.0 + - - -
167B LEU* 3.8 28.7 - - + +
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL* 3.4 24.3 - - - +
106A SER 4.9 1.4 - - - +
108A PRO* 3.7 36.9 - - + +
109A ARG* 5.7 6.1 + - - +
131B ARG* 2.9 49.6 + - + +
134B LYS* 1.3 80.6 - - + +
136B LEU* 1.3 63.9 + - + +
137B GLY 3.4 0.6 + - - -
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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