Contacts of the helix formed by residues 154 - 159 (chain B) in PDB entry 2IG7
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 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B ARG* 3.6 30.9 - - - +
152B PRO 4.7 2.3 + - - +
153B LEU* 1.3 78.2 - - - +
155B THR* 1.3 66.2 + - - +
156B GLN* 4.4 5.4 - - + +
157B GLU* 2.8 40.8 + - + +
158B LEU* 3.6 3.5 + - - +
245B GLU* 3.9 7.4 - - - +
289B THR* 6.2 5.8 - - + -
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Residues in contact with THR 155 (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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154B LYS* 1.3 71.6 - - - +
156B GLN* 1.3 73.3 + - - +
158B LEU* 3.1 23.3 + - - +
159B ARG* 4.3 2.8 + - - -
245B GLU* 2.9 27.1 + - - +
283B GLU 3.8 7.2 - - - +
284B TRP* 3.4 27.2 - - - +
285B VAL 4.8 0.9 - - - -
286B TYR 3.3 23.5 + - - +
287B ASP* 3.4 29.4 + - + -
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Residues in contact with GLN 156 (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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154B LYS* 3.3 4.4 - - + +
155B THR* 1.3 90.9 - - - +
157B GLU* 1.3 60.4 + - + +
159B ARG* 2.9 53.1 + - - +
160B GLU* 4.1 4.0 + - - +
284B TRP 4.9 1.0 + - - -
287B ASP* 5.5 3.4 + - - +
299B ARG* 4.6 14.2 - - - +
302B ASP* 3.3 25.0 + - - +
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Residues in contact with GLU 157 (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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151B ARG* 2.8 40.9 + - - -
153B LEU* 3.5 11.0 - - + +
154B LYS* 2.8 46.0 + - + +
156B GLN* 1.3 73.8 - - + +
158B LEU* 1.3 65.2 + - - +
159B ARG 3.1 3.6 + - - -
160B GLU* 3.1 38.6 + - - +
163B LEU* 3.7 28.3 - - + +
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Residues in contact with LEU 158 (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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153B LEU* 4.0 11.9 - - + -
154B LYS 4.0 5.6 - - - +
155B THR 3.1 15.7 + - - +
157B GLU* 1.3 77.4 - - - +
159B ARG* 1.4 59.1 + - - +
160B GLU 3.4 0.7 - - - -
164B SER* 3.5 16.6 - - - -
167B ILE* 3.7 27.7 - - + +
245B GLU* 3.5 41.5 - - + +
248B ILE* 4.0 4.9 - - + -
280B HIS* 4.0 14.9 + - + -
283B GLU* 3.9 18.6 - - + +
284B TRP* 3.3 41.5 + - + +
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Residues in contact with ARG 159 (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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155B THR 4.3 2.2 + - - -
156B GLN* 2.9 44.3 + - - +
157B GLU 3.1 0.8 - - - -
158B LEU* 1.4 78.3 - - - +
160B GLU* 1.3 67.1 + - + +
161B PRO* 3.3 8.3 - - - +
164B SER* 4.8 1.6 - - - -
284B TRP* 3.5 38.0 + - + -
301B THR 5.4 0.4 + - - -
302B ASP* 2.6 60.1 + - - +
308B GLN* 3.7 30.7 + - - +
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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