Contacts of the strand formed by residues 144 - 148 (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 ALA 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B ASP* 1.3 76.4 - - - +
145B PHE* 1.3 67.7 + - - +
165B VAL* 4.4 0.4 - - - -
166B GLN* 3.3 17.3 - - + +
168B ILE* 3.5 20.0 - - + -
197B ILE* 3.5 27.6 - - + -
198B LYS 2.7 12.4 + - - +
199B VAL* 3.4 7.0 - - - -
200B LYS* 3.1 25.6 + - - +
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Residues in contact with PHE 145 (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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135B ILE* 4.3 23.6 - - + -
138B LEU* 4.3 20.4 - - + -
139B ALA* 4.0 27.8 - - + -
144B ALA* 1.3 82.9 - - - +
146B LEU* 1.3 63.1 + - - +
147B VAL* 3.8 1.0 + - + -
165B VAL* 4.4 5.6 - - + -
166B GLN 2.8 10.7 + - - +
167B LEU* 3.4 19.0 - - + +
168B ILE* 2.9 24.2 + - - -
200B LYS 4.1 4.0 - - - -
201B GLY* 3.6 26.9 - - - -
202B LEU 3.5 22.4 - - - -
203B ILE* 3.9 19.3 - - + -
233B HIS* 4.8 0.9 - - + -
235B VAL* 4.0 24.2 - - + -
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Residues in contact with LEU 146 (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* 1.3 73.3 - - - +
147B VAL* 1.3 62.9 + - - +
168B ILE* 3.2 38.8 - - + +
170B ILE* 4.0 11.0 - - + -
185B VAL* 4.8 4.0 - - + +
188B ALA* 4.1 20.0 - - + +
189B TYR* 3.9 29.2 - - + +
199B VAL* 3.6 28.3 - - + -
201B GLY 3.0 12.6 + - - +
202B LEU* 3.3 21.3 - - + +
203B ILE* 3.0 25.6 + - - +
226B PHE* 4.9 3.1 - - + -
232B ILE* 4.8 6.1 - - + -
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Residues in contact with VAL 147 (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 4.0 1.8 - - - +
146B LEU* 1.3 79.9 - - - +
148B PRO* 1.3 84.9 - - + +
151B TYR* 3.6 29.5 - - + -
155B PHE* 4.1 11.9 - - + -
159B LEU* 4.7 1.6 - - + -
167B LEU* 3.6 35.2 - - + -
168B ILE 3.0 8.2 + - - +
169B PRO* 3.2 8.0 - - + +
170B ILE* 2.9 21.9 + - - +
203B ILE* 3.5 22.9 - - + +
205B THR* 5.9 0.4 - - - +
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Residues in contact with PRO 148 (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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146B LEU 4.4 1.3 - - - +
147B VAL* 1.3 86.8 - - + +
149B SER* 1.3 60.1 + - - +
150B PRO 3.6 3.3 - - - +
151B TYR* 3.1 23.4 - - - +
170B ILE* 3.6 28.3 - - + +
172B CYS* 4.6 5.2 - - - -
180B ILE* 3.7 24.0 - - + -
202B LEU* 4.8 1.8 - - + -
203B ILE 3.4 19.5 - - - +
204B LEU* 3.3 28.3 - - + -
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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