Contacts of the strand formed by residues 164 - 171 (chain A) in PDB entry 2IAU
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 MET 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 3.9 25.4 - - + +
106A ILE* 4.2 3.1 - - + -
107A ALA* 4.1 23.1 - - + -
109A LYS 4.5 0.9 - - - +
110A ASP* 3.0 19.5 - - + +
111A SER* 2.7 31.9 + - - +
116A MET* 3.7 43.1 - - + -
132A ILE* 4.1 8.1 - - + -
156A TYR* 3.9 23.6 - - + -
157A CYS 4.0 0.2 - - - -
158A PHE* 3.9 26.0 - - + -
162A GLY 3.9 2.6 + - - -
163A GLN* 1.3 69.2 - - - +
165A ILE* 1.3 57.1 + - - +
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Residues in contact with ILE 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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111A SER* 3.7 19.3 - - - +
156A TYR* 3.2 2.9 - - - -
157A CYS 2.8 40.5 + - - +
159A THR* 4.5 3.8 - - + -
163A GLN* 3.8 27.6 - - + -
164A MET* 1.3 71.7 - - - +
166A GLN* 1.3 75.2 + - - +
167A VAL* 3.2 13.4 + - + +
209A ALA* 3.7 26.2 - - + +
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Residues in contact with GLN 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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110A ASP* 3.9 9.2 + - - +
111A SER* 4.7 1.6 + - - -
114A ARG* 3.7 39.4 + - - +
115A ARG 5.8 0.4 + - - -
117A GLN* 3.5 6.5 + - - -
154A SER* 3.4 21.4 + - - -
155A ILE 3.5 6.7 - - - +
156A TYR* 3.3 37.8 + - + -
164A MET 3.9 2.2 + - - -
165A ILE* 1.3 78.6 - - - +
167A VAL* 1.3 58.7 + - - +
168A ASP 3.6 18.4 - - - +
169A THR* 4.2 12.6 - - - +
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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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131A TRP* 4.4 6.7 - - + -
155A ILE* 2.8 35.9 + - + +
156A TYR 4.1 6.7 - - - +
157A CYS* 3.9 14.8 - - + -
165A ILE* 3.2 17.0 + - + +
166A GLN* 1.3 74.6 - - - +
168A ASP* 1.3 66.0 + - - +
209A ALA* 3.5 28.5 - - - +
211A ILE* 3.5 35.7 - - + +
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Residues in contact with ASP 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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154A SER* 3.4 3.8 - - - -
155A ILE* 2.8 34.4 + - + +
166A GLN* 3.5 6.5 - - - +
167A VAL* 1.3 80.5 - - - +
169A THR* 1.3 91.2 + - - +
171A PHE* 4.1 4.7 - - + -
203A TYR* 2.6 41.5 + - + +
211A ILE* 4.7 1.1 - - + -
214A LYS* 3.5 15.8 + - - +
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Residues in contact with THR 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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117A GLN* 4.8 0.2 + - - -
152A PHE* 4.0 7.1 + - - -
153A GLY 3.3 12.7 + - - -
154A SER* 2.7 22.7 + - - +
166A GLN* 4.2 13.4 + - - +
168A ASP* 1.3 90.8 + - - +
170A ALA* 1.3 81.9 + - + +
171A PHE* 3.4 11.1 - - - -
214A LYS* 4.0 4.7 + - - -
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Residues in contact with ALA 170 (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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151A LYS* 3.3 41.4 + - + +
153A GLY 3.1 1.8 + - - +
169A THR* 1.3 92.6 + - + +
171A PHE* 1.3 61.5 + - - +
194A GLU* 4.6 1.4 - - - +
214A LYS* 4.9 6.4 + - - +
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Residues in contact with PHE 171 (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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147A SER* 3.7 1.0 + - - -
151A LYS* 3.4 2.6 - - - -
152A PHE 3.4 6.9 + - - -
153A GLY 2.9 27.9 + - - +
155A ILE* 3.6 26.2 - - + -
168A ASP* 3.9 5.6 - - - -
169A THR 3.5 23.6 - - - -
170A ALA* 1.3 80.2 - - - +
172A GLN* 1.3 60.1 + - - +
173A PHE 3.3 3.7 + - - -
174A PRO* 3.5 27.4 - - + -
192A VAL* 4.4 7.4 - - + -
194A GLU* 3.6 22.0 - - + -
201A TRP* 3.8 29.6 - + + -
203A TYR* 2.9 35.9 - + - -
214A LYS* 3.7 17.0 - - - -
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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