Contacts of the strand formed by residues 169 - 177 (chain B) in PDB entry 2IDW
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 HIS 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A PHE* 3.7 42.6 - + - -
164B ILE 3.8 0.2 - - - +
165B GLU* 3.4 4.1 - - - -
166B ILE* 2.8 37.5 + - - +
167B ALA 3.3 17.5 - - - -
168B GLY* 1.3 81.3 - - - +
170B LYS* 1.3 62.1 + - - +
171B ALA 3.8 0.5 + - - -
193B ILE* 3.6 28.6 + - + +
703B PO4 2.7 35.0 + - - -
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Residues in contact with LYS 170 (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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163B ILE* 3.7 26.8 - - + +
164B ILE 3.8 4.9 - - - +
165B GLU* 3.9 20.1 - - + +
168B GLY 4.3 0.4 + - - -
169B HIS* 1.3 73.1 - - - +
171B ALA* 1.3 76.2 + - - +
172B ILE* 4.4 16.8 - - + +
192B GLN* 4.4 8.1 - - - +
193B ILE* 4.0 8.3 - - - +
606B ACY 4.5 13.3 + - - -
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 3.6 0.2 - - - -
164B ILE* 2.9 48.2 + - + +
166B ILE* 4.1 16.8 - - + -
170B LYS* 1.3 76.4 - - - +
172B ILE* 1.3 70.1 + - - +
189B LEU* 4.1 8.5 - - + -
192B GLN* 3.2 26.7 - - + +
193B ILE* 4.3 2.2 - - + -
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Residues in contact with ILE 172 (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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161B GLN* 3.7 38.3 - - + +
162B ILE 3.2 7.4 - - - +
163B ILE* 4.0 23.3 - - + +
170B LYS* 4.4 18.2 - - + -
171B ALA* 1.3 80.8 - - - +
173B GLY* 1.3 59.5 + - - +
189B LEU* 4.5 0.2 - - - -
192B GLN* 2.8 28.8 + - - +
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Residues in contact with GLY 173 (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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159B TYR 3.9 0.2 - - - +
161B GLN* 3.4 12.1 + - - -
162B ILE* 2.9 33.2 + - - +
172B ILE* 1.3 76.7 - - - +
174B THR* 1.3 64.8 + - - -
175B VAL* 4.0 1.7 - - - +
188B ASN* 4.9 0.4 - - - -
189B LEU* 3.9 16.3 - - - +
192B GLN* 4.1 3.1 - - - -
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Residues in contact with THR 174 (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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131B THR* 3.9 9.4 + - - +
158B GLN* 3.7 25.7 + - + +
159B TYR 3.3 5.8 - - - +
160B ASP* 3.1 28.8 + - - +
161B GLN 4.7 0.5 + - - -
173B GLY* 1.3 73.1 - - - -
175B VAL* 1.3 65.3 + - - +
176B LEU* 4.1 11.4 - - + -
188B ASN* 2.9 30.6 + - - +
189B LEU* 4.6 0.7 - - - +
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Residues in contact with VAL 175 (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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115B ILE* 3.9 16.2 - - + -
131B THR* 3.9 15.0 - - + -
133B ILE* 3.6 30.5 - - + -
138B LEU* 4.7 1.1 - - + -
157B ARG 3.5 2.1 - - - +
159B TYR* 2.9 37.1 + - + +
162B ILE* 4.1 22.0 - - + -
164B ILE* 4.7 5.6 - - + -
173B GLY 4.0 8.5 - - - +
174B THR* 1.3 80.1 - - - +
176B LEU* 1.3 67.4 + - - +
177B VAL* 4.0 11.6 + - + -
189B LEU* 4.5 9.0 - - + -
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Residues in contact with LEU 176 (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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130B ASP* 3.9 28.3 - - + +
131B THR 2.9 16.2 + - - +
132B VAL* 3.2 11.5 - - + +
133B ILE* 2.8 25.6 + - - +
145B LYS* 5.2 1.1 - - + -
146B MET 5.9 0.4 - - - +
147B ILE* 4.2 24.7 - - + -
156B VAL* 4.0 26.5 - - + -
157B ARG 3.4 2.5 - - - -
158B GLN* 3.6 41.7 - - + +
174B THR* 4.1 8.7 - - + -
175B VAL* 1.3 73.5 - - - +
177B VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 177 (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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133B ILE* 3.2 8.3 - - + +
134B GLU 3.6 18.4 - - - +
135B GLU* 3.4 27.0 - - - +
136B MET* 3.9 6.5 - - + +
138B LEU* 4.0 18.4 - - + -
156B VAL* 3.3 4.4 - - - -
157B ARG* 2.9 51.5 + - + +
159B TYR* 3.8 27.8 - - + -
175B VAL* 4.0 9.9 - - + -
176B LEU* 1.3 75.6 - - - +
178B GLY* 1.3 61.4 + - - +
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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