Contacts of the helix formed by residues 155 - 169 (chain A) in PDB entry 1IC8
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 LYS 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A MET* 1.3 72.0 - - - +
156A THR* 1.3 68.6 + - - +
157A GLN* 3.3 6.3 - - + +
158A LYS* 2.9 17.6 + - + +
159A ARG 3.0 11.1 + - - -
405F G 3.5 33.4 + - - +
406F T 2.9 33.2 + - - +
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Residues in contact with THR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.5 28.4 + - + +
154A MET 3.5 1.4 + - - -
155A LYS* 1.3 72.6 - - - +
157A GLN* 1.3 60.2 + - - +
159A ARG* 3.1 26.6 + - - +
160A ALA* 2.7 29.2 + - + +
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Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LYS* 3.3 5.1 - - + +
156A THR* 1.3 79.2 - - - +
158A LYS* 1.3 68.4 + - + +
160A ALA* 3.0 21.2 - - + +
161A ALA* 3.1 6.8 + - - +
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Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLY 5.9 0.7 - - - +
139A LEU* 3.4 24.3 - - + +
143A HIS* 4.6 4.5 - - + +
154A MET* 3.4 26.0 - - + -
155A LYS* 2.9 10.8 + - + +
157A GLN* 1.3 73.7 - - + +
159A ARG* 1.3 54.3 + - - +
160A ALA 2.6 3.9 + - - -
161A ALA* 2.4 39.8 + - - +
162A LEU 3.1 2.6 + - - -
406F T 2.5 60.7 + - - +
407F G 5.0 9.2 + - - -
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Residues in contact with ARG 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU 6.0 0.2 - - - -
108A LEU* 3.6 30.7 + - + +
110A GLU 5.8 0.4 + - - -
112A PRO* 3.0 34.4 - - - +
147A HIS* 4.0 14.6 - - - +
154A MET* 3.3 50.5 + - + +
155A LYS 3.0 3.0 + - - +
156A THR* 3.6 27.8 + - - +
158A LYS* 1.3 79.2 - - - +
160A ALA* 1.3 56.9 + - - +
162A LEU* 3.7 3.6 - - - +
163A TYR* 2.8 66.4 + - + -
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A VAL* 4.4 4.2 - - + +
108A LEU* 3.6 26.9 - - + +
156A THR* 2.7 16.2 + - + +
157A GLN* 3.0 20.6 - - + +
158A LYS 2.6 4.2 + - - -
159A ARG* 1.3 72.3 - - - +
161A ALA* 1.3 57.4 + - - -
163A TYR* 4.0 0.5 - - - +
164A THR* 2.8 33.6 + - - +
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A THR* 3.5 37.2 - - - +
139A LEU* 4.2 6.1 - - + -
157A GLN 3.1 8.8 + - - +
158A LYS* 2.4 31.5 + - - +
160A ALA* 1.3 68.0 - - - +
162A LEU* 1.3 59.8 + - - +
164A THR* 3.7 4.8 - - - -
165A TRP* 3.2 17.3 + - - +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ALA* 5.9 1.6 - - - -
119A VAL* 3.9 27.8 - - + -
133A VAL* 3.9 26.2 - - + -
137A THR* 4.3 2.5 - - - -
139A LEU* 3.9 14.8 - - + +
144A LEU* 4.1 11.7 - - + -
147A HIS* 4.3 10.3 - - + +
148A LEU* 3.8 28.0 - - + -
154A MET* 5.2 2.2 - - - -
158A LYS 3.1 2.6 + - - +
159A ARG* 3.7 9.4 - - - +
161A ALA* 1.3 78.1 - - - +
163A TYR* 1.3 83.8 + - + +
164A THR 3.1 0.7 + - - -
165A TRP* 3.1 8.1 + - + +
166A TYR* 2.8 23.6 + - - +
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Residues in contact with TYR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A VAL* 4.2 16.4 - - + -
107A LEU* 3.3 40.2 - - + -
108A LEU* 3.3 26.5 - - + -
112A PRO* 3.6 22.0 + - - +
115A VAL* 3.4 28.7 - - + +
116A ALA* 5.4 0.4 - - - -
119A VAL* 4.9 4.3 - - + -
147A HIS* 4.4 3.6 + - - -
159A ARG* 2.8 49.7 + - + +
160A ALA 4.0 2.2 - - - +
162A LEU* 1.3 88.7 - - + +
164A THR* 1.3 63.7 + - - +
166A TYR* 3.2 11.1 - - - +
167A VAL* 2.9 27.2 + - - +
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Residues in contact with THR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLN* 6.5 0.7 - - + -
104A VAL* 3.9 21.5 - - + +
160A ALA* 2.8 25.4 + - - +
161A ALA* 3.7 6.2 - - - -
163A TYR* 1.3 72.9 - - - +
165A TRP* 1.3 70.7 + - - +
167A VAL* 2.7 16.5 + - + +
168A ARG* 2.8 47.1 + - + +
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Residues in contact with TRP 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A VAL* 5.1 2.0 - - + -
122A TYR* 5.4 0.9 - + - -
123A LEU* 3.6 24.5 - - + -
128A ILE* 3.9 13.9 - - + -
132A GLU* 4.3 14.8 + - - +
133A VAL* 3.5 39.7 - - + -
136A THR* 3.1 31.5 + - - +
137A THR* 3.6 13.0 - - + -
161A ALA 3.2 10.8 + - - +
162A LEU* 3.1 13.6 + - + +
164A THR* 1.3 80.8 - - - +
166A TYR* 1.3 86.9 + + + +
168A ARG* 3.2 8.8 + - - +
169A LYS* 2.7 70.3 + - + +
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 4.8 13.0 - - + -
115A VAL* 5.6 0.7 - - + -
118A MET* 4.0 32.9 + - + +
119A VAL* 3.8 39.7 - - + -
122A TYR* 3.9 40.2 - + + +
162A LEU 2.8 12.6 + - - +
163A TYR* 3.2 15.3 - - + +
164A THR 2.8 0.4 + - - -
165A TRP* 1.3 92.2 - + + +
167A VAL* 1.3 70.0 + - + +
169A LYS* 3.1 13.3 + - - +
170A GLN* 2.8 27.6 + - - +
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A HIS* 6.3 0.9 - - + -
100A GLN* 3.9 40.6 + - + +
103A VAL* 3.6 31.4 - - + -
104A VAL* 4.6 5.4 - - + -
107A LEU* 4.4 9.2 - - + -
163A TYR 2.9 18.4 + - - +
164A THR* 2.7 13.7 + - - +
166A TYR* 1.3 79.4 - - + +
168A ARG* 1.3 58.9 + - - +
169A LYS 3.5 0.2 + - - -
170A GLN* 3.8 19.8 + - - +
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Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLN* 3.7 26.2 + - - +
101A LYS* 5.1 9.9 - - - +
164A THR* 2.8 44.5 + - + +
165A TRP* 3.5 7.8 - - - +
167A VAL* 1.3 70.0 - - - +
169A LYS* 1.3 63.9 + - - +
170A GLN 3.1 3.7 + - - -
171A ARG* 3.0 49.7 + - - +
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Residues in contact with LYS 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TYR* 4.0 11.2 - - + +
128A ILE* 3.8 19.2 - - - +
132A GLU* 2.6 32.0 + - - +
165A TRP* 2.7 44.9 + - + +
166A TYR* 3.1 15.0 + - - +
168A ARG* 1.3 73.9 - - - +
170A GLN* 1.3 60.7 + - - +
171A ARG* 2.4 37.3 + - + +
172A GLU* 2.8 27.8 + - - +
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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