Contacts of the helix formed by residues 193 - 205 (chain A) in PDB entry 1IX9
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 ASN 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A LYS 3.2 19.1 + - - +
87A GLY* 2.9 30.1 + - - +
88A LEU 3.6 9.4 + - - +
89A LYS* 3.5 29.3 - - - +
92A THR* 3.5 8.4 - - - +
164A MET* 5.7 0.5 - - - +
191A VAL 3.2 2.1 + - - -
192A VAL* 1.3 71.4 - - - +
194A TRP* 1.3 63.6 + - - +
195A ASP* 3.0 21.9 + - - +
196A GLU* 3.1 16.1 + - + +
197A ALA* 3.1 19.8 + - - +
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Residues in contact with TRP 194 (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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92A THR* 3.0 30.7 + - - +
93A THR 4.0 4.9 - - - +
94A LEU* 3.6 69.3 - - + +
98A LEU* 3.9 11.4 - - + +
102A ILE* 4.2 6.7 - - + -
112A PHE* 3.8 24.5 - + - -
113A LYS* 4.7 8.9 - - - +
131A LEU* 4.6 2.9 - - + -
164A MET* 4.1 20.9 - - + -
189A TRP* 4.0 17.8 + + - -
192A VAL* 3.1 31.7 + - + +
193A ASN* 1.3 71.5 - - - +
195A ASP* 1.3 56.8 + - - +
197A ALA* 3.7 17.0 - - + +
198A ALA* 2.8 30.1 + - - +
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Residues in contact with ASP 195 (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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89A LYS* 2.8 28.9 + - - +
92A THR* 3.6 19.9 - - - +
93A THR 4.7 6.9 + - - +
95A GLN* 4.9 5.9 + - - -
193A ASN* 3.0 9.7 + - - +
194A TRP* 1.3 78.2 - - - +
196A GLU* 1.3 56.2 + - - +
198A ALA* 3.4 6.1 + - - +
199A ALA* 3.0 27.4 + - - +
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Residues in contact with GLU 196 (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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86A LYS* 3.5 46.5 - - + +
87A GLY* 4.6 4.0 - - - -
193A ASN* 3.1 19.9 + - + +
195A ASP* 1.3 73.4 - - - +
197A ALA* 1.3 67.4 + - - +
199A ALA* 3.2 11.2 + - - +
200A ARG* 2.9 49.3 + - - +
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Residues in contact with ALA 197 (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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98A LEU* 3.6 19.5 - - + -
163A ILE* 3.6 32.0 - - + +
164A MET* 4.4 9.0 - - + -
193A ASN 3.1 15.9 + - - +
194A TRP* 3.7 17.0 - - + +
196A GLU* 1.3 77.9 - - - +
198A ALA* 1.3 56.6 + - - +
200A ARG* 3.4 0.7 + - - +
201A PHE* 2.9 30.3 + - - +
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Residues in contact with ALA 198 (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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95A GLN* 5.5 6.7 - - + +
98A LEU* 3.8 19.0 - - + +
194A TRP 2.8 19.0 + - - +
195A ASP* 3.6 7.6 - - - +
197A ALA* 1.3 75.4 - - - +
199A ALA* 1.3 58.2 + - - +
201A PHE* 3.3 5.1 + - - +
202A ALA* 2.8 30.5 + - - +
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Residues in contact with ALA 199 (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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195A ASP 3.0 16.7 + - - +
196A GLU* 3.6 16.2 - - - +
198A ALA* 1.3 77.3 - - - +
200A ARG* 1.3 60.0 + - - +
202A ALA* 3.3 7.2 + - - +
203A ALA* 3.1 22.3 + - - +
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Residues in contact with ARG 200 (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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83A LEU* 3.5 26.9 - - - +
86A LYS* 6.3 0.6 - - - +
150A LEU* 5.7 2.6 - - - +
161A PHE* 3.3 36.3 - - + -
162A PRO* 2.8 35.0 + - - +
163A ILE* 3.5 21.1 + - + +
196A GLU* 2.9 41.1 + - - +
197A ALA 3.7 3.8 - - - +
199A ALA* 1.3 76.4 - - - +
201A PHE* 1.3 61.2 + - - +
203A ALA* 3.3 6.1 + - - +
204A LYS* 3.2 28.4 + - - +
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Residues in contact with PHE 201 (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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97A ASP* 3.7 23.6 - - + -
98A LEU* 3.8 30.7 - - + -
101A ALA* 3.5 21.5 - - + -
104A ARG* 5.0 6.5 - - - -
133A LEU* 4.3 15.7 - - + -
138A LEU* 4.2 19.1 - - + -
163A ILE* 3.8 20.8 - - + +
197A ALA 2.9 17.8 + - - +
198A ALA* 3.6 6.1 - - - +
199A ALA 3.3 0.2 - - - -
200A ARG* 1.3 77.5 - - - +
202A ALA* 1.3 58.4 + - - +
204A LYS* 4.6 0.4 - - - +
205A LYS* 2.8 70.6 + - + +
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Residues in contact with ALA 202 (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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198A ALA 2.8 17.7 + - - +
199A ALA* 3.6 8.5 - - - +
201A PHE* 1.3 77.8 - - - +
203A ALA* 1.3 62.2 + - - +
204A LYS 3.4 0.5 + - - -
205A LYS* 4.0 28.4 - - - +
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Residues in contact with ALA 203 (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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161A PHE* 6.2 0.7 - - + -
199A ALA 3.1 13.2 + - - +
200A ARG* 3.7 10.5 - - - +
201A PHE 3.2 0.2 - - - -
202A ALA* 1.3 77.4 - - - +
204A LYS* 1.4 69.7 + - + +
205A LYS 5.1 1.0 - - - +
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Residues in contact with LYS 204 (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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133A LEU* 3.5 22.8 - - + +
135A GLY 4.8 2.4 - - - +
161A PHE* 3.6 56.4 - - + +
200A ARG 3.2 10.0 + - - +
201A PHE* 3.1 2.7 + - - +
203A ALA* 1.4 88.3 - - + +
205A LYS* 1.3 66.4 + - - +
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Residues in contact with LYS 205 (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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97A ASP* 3.4 27.9 + - + +
133A LEU* 4.1 9.6 - - - +
135A GLY 5.0 2.1 - - - +
136A ASP* 3.7 18.9 - - - +
201A PHE* 2.8 59.9 + - + +
202A ALA* 4.0 25.5 - - - +
203A ALA 3.8 1.3 - - - +
204A LYS* 1.3 77.5 - - - +
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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