Contacts of the strand formed by residues 199 - 205 (chain B) in PDB entry 1IAX
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 VAL 199 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144B ALA 3.4 7.4 - - - +
146B LEU* 3.6 33.7 - - + -
168B ILE* 4.7 9.4 - - + -
189B TYR* 3.8 25.8 + - + -
192B ALA* 3.4 24.5 - - + -
193B GLN* 5.3 2.0 - - + +
197B ILE 3.0 14.3 + - - +
198B LYS* 1.3 72.1 - - - +
200B LYS* 1.3 60.7 + - - +
201B GLY 3.8 13.9 - - - +
232B ILE* 3.2 20.5 - - + +
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Residues in contact with LYS 200 (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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11A ILE* 4.3 21.1 + - + +
12A LEU 4.0 16.4 + - - -
13A SER* 4.6 0.6 - - - +
138B LEU 3.2 26.3 + - - +
139B ALA* 4.1 3.4 - - + -
140B ASP* 3.4 19.8 + - - -
143B ASP* 2.9 36.2 + - - +
144B ALA 3.1 7.8 + - - +
145B PHE* 4.1 10.3 - - + -
198B LYS* 4.3 21.7 - - + +
199B VAL* 1.3 77.0 - - - +
201B GLY* 1.3 56.7 + - - +
232B ILE* 3.7 8.5 - - - +
233B HIS* 3.0 30.0 + - + +
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Residues in contact with GLY 201 (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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145B PHE* 3.5 21.9 - - - -
146B LEU* 3.0 24.1 + - - +
199B VAL* 3.5 8.5 - - - +
200B LYS* 1.3 81.4 - - - +
202B LEU* 1.3 62.3 + - - +
232B ILE* 4.1 8.4 - - - +
233B HIS 3.0 16.2 - - - -
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Residues in contact with LEU 202 (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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145B PHE* 3.5 3.0 - - - -
146B LEU* 3.3 24.2 - - + +
148B PRO* 4.8 1.3 - - + -
170B ILE* 3.8 25.4 - - + -
180B ILE* 6.2 0.7 - - + -
185B VAL* 4.3 14.6 - - + -
201B GLY* 1.3 75.4 - - - +
203B ILE* 1.3 64.8 + - - +
204B LEU* 3.6 27.1 - - + -
223B VAL* 4.0 18.2 - - + -
226B PHE* 5.6 2.7 - - + -
227B THR* 4.6 10.3 - - - +
232B ILE* 5.6 2.5 - - + -
233B HIS 2.8 7.9 + - - +
234B LEU* 3.5 22.0 - - + -
235B VAL* 2.8 24.9 + - - +
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Residues in contact with ILE 203 (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 ASN* 4.4 3.8 - - + +
134B ILE* 5.4 1.6 - - + -
135B ILE* 5.1 4.9 - - + -
145B PHE* 3.9 11.6 - - + -
146B LEU 3.0 5.2 + - - +
147B VAL* 3.5 34.3 - - + +
148B PRO* 3.4 17.3 - - - +
155B PHE* 3.9 26.6 - - + -
159B LEU* 4.1 25.6 - - + -
202B LEU* 1.3 75.1 - - - +
204B LEU* 1.3 67.2 + - - +
205B THR* 4.7 1.7 + - - -
235B VAL* 3.1 34.8 - - + +
237B ASP* 4.0 9.6 - - - +
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Residues in contact with LEU 204 (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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148B PRO* 3.3 32.1 - - + -
180B ILE* 3.4 16.8 - - + -
202B LEU* 3.6 20.5 - - + +
203B ILE* 1.3 75.2 - - - +
205B THR* 1.3 69.2 + - - +
206B ASN* 5.0 1.8 - - + +
215B LEU* 3.5 26.9 - - + -
220B LEU* 3.7 20.4 - - + -
223B VAL* 4.4 16.6 - - + -
234B LEU* 4.2 6.5 - - + -
235B VAL 2.7 11.3 + - - +
236B CYS* 4.6 9.6 - - - -
237B ASP* 2.8 29.2 + - - +
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Residues in contact with THR 205 (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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147B VAL* 5.9 0.3 - - - +
151B TYR* 5.7 2.4 - - - +
152B TYR* 5.6 1.3 + - + +
155B PHE* 3.8 23.7 - - - -
203B ILE 4.7 0.5 + - - -
204B LEU* 1.3 80.0 + - - +
206B ASN* 1.3 60.6 + - - +
207B PRO 3.5 14.4 - - - +
208B SER* 3.4 17.9 + - - -
209B ASN* 4.0 20.7 + - + +
215B LEU* 4.5 6.6 - - - +
237B ASP* 3.2 14.8 - - + +
239B ILE* 5.4 0.4 - - + -
240B TYR* 4.9 2.7 - - + -
501B PLP 4.0 26.7 - - + -
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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