Contacts of the helix formed by residues 174 - 182 (chain A) in PDB entry 2I9W
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 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A GLN 4.1 7.0 - - - +
164A LYS* 3.5 28.0 - - + +
165A GLN 3.6 7.6 - - - -
166A PRO* 4.5 0.4 - - - -
172A GLY 3.9 0.8 + - - -
173A GLU* 1.3 74.3 - - - +
175A PHE* 1.3 68.0 + - - +
176A LYS* 4.1 19.0 - - + +
177A ARG* 2.8 29.3 + - + +
178A CYS* 3.2 8.9 + - - +
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Residues in contact with PHE 175 (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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159A MSE 6.0 0.9 - - - -
161A VAL* 3.5 37.9 - - + -
162A THR 3.9 6.5 - - - +
163A GLN* 3.5 42.1 + - - +
165A GLN 3.0 16.1 + - - +
166A PRO 4.7 0.4 - - - +
167A CYS* 3.8 27.5 - - - +
168A ILE* 4.0 25.6 - - + -
173A GLU 3.4 1.4 + - - -
174A LYS* 1.3 69.8 - - - +
176A LYS* 1.3 56.2 + - - +
178A CYS 3.0 12.5 + - - -
179A CYS* 4.2 4.9 - - + -
180A GLY* 2.9 50.3 + - - -
183A ILE* 4.4 16.6 - - + -
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Residues in contact with LYS 176 (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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163A GLN* 3.1 47.9 + - + +
164A LYS* 4.5 21.7 - - + +
174A LYS* 4.1 16.2 - - + +
175A PHE* 1.3 75.3 - - - +
177A ARG* 1.3 67.4 - - + +
178A CYS 3.4 1.1 - - - -
180A GLY* 4.6 5.5 - - - -
181A MSE 3.3 25.7 + - - +
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Residues in contact with ARG 177 (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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112A ARG* 5.9 0.5 + - - -
173A GLU* 4.4 12.6 - - + +
174A LYS* 2.8 31.7 + - + +
176A LYS* 1.3 85.6 - - + +
178A CYS* 1.3 59.9 + - - +
181A MSE 4.0 14.8 - - - +
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Residues in contact with CYS 178 (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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112A ARG* 3.7 24.2 - - - -
113A HIS* 3.9 11.2 - - - -
167A CYS* 3.6 7.9 - - + -
171A SER* 3.3 18.4 - - - -
173A GLU* 4.0 8.3 - - + -
174A LYS 3.5 11.7 - - - +
175A PHE 3.0 2.8 + - - -
176A LYS 3.4 1.0 + - - -
177A ARG* 1.3 81.6 - - - +
179A CYS* 1.3 66.0 + - - +
180A GLY 3.2 1.1 - - - -
181A MSE 3.1 20.3 + - - +
182A TYR* 3.7 7.7 - - - -
201A ZN 2.4 32.5 - - - -
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Residues in contact with CYS 179 (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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76A LEU* 5.3 0.4 - - - -
113A HIS* 3.3 21.8 - - - -
138A VAL* 3.9 3.8 - - - -
153A LEU* 3.8 29.9 - - + +
167A CYS* 3.5 9.9 - - - -
168A ILE* 4.9 2.9 - - + -
169A CYS* 3.7 14.1 - - - -
175A PHE* 4.2 8.7 - - + -
178A CYS* 1.3 78.5 - - - +
180A GLY* 1.3 57.0 + - - +
182A TYR* 3.0 8.2 + - - +
183A ILE* 2.9 30.7 + - + +
201A ZN 2.4 33.0 - - - -
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Residues in contact with GLY 180 (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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163A GLN* 5.3 1.9 - - - +
175A PHE* 2.9 40.6 + - - -
176A LYS* 4.6 6.5 - - - -
179A CYS* 1.3 74.3 - - - +
181A MSE 1.3 60.2 + - - +
182A TYR 3.1 2.0 - - - -
183A ILE* 3.1 20.6 - - - +
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Residues in contact with MSE 181 (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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175A PHE 4.1 1.2 + - - -
176A LYS 3.3 22.8 + - - +
177A ARG* 4.0 14.8 - - - +
178A CYS 3.1 24.7 + - - +
180A GLY* 1.3 76.6 - - - +
182A TYR* 1.3 86.1 + - + +
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Residues in contact with TYR 182 (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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109A LEU* 3.5 38.0 + - + +
110A SER* 3.8 17.8 - - - -
113A HIS* 3.5 40.2 - + + -
115A GLN* 4.3 7.6 + - - +
136A THR* 3.8 28.7 + - + +
153A LEU* 4.6 1.8 - - + -
155A PRO* 5.7 0.9 - - - +
178A CYS* 3.7 12.6 - - - -
179A CYS 3.0 4.5 + - - +
181A MSE 1.3 108.1 - - + +
183A ILE* 1.3 65.0 + - - +
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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