Contacts of the strand formed by residues 270 - 275 (chain A) 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 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A LEU* 3.6 30.7 - - + -
227A THR* 5.5 0.4 - - + -
234A LEU* 3.5 9.0 - - + +
253A ILE* 3.9 25.8 - - + -
257A LEU* 3.8 36.6 - - + -
265A CYS* 6.2 0.2 - - + -
266A ASN 4.3 10.1 - - - +
267A LYS 3.7 4.6 + - - +
268A ASP 3.5 1.6 - - - -
269A LEU* 1.3 82.6 - - + +
271A HIS* 1.3 73.6 + - - +
293A PHE* 3.2 34.1 + - + +
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Residues in contact with HIS 271 (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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134A ILE* 4.1 20.6 - - + -
138A LEU* 3.6 31.4 - - + +
233A HIS* 2.9 25.5 - + + -
234A LEU 3.0 15.6 + - - +
235A VAL* 4.3 3.8 - - + -
236A CYS* 2.8 27.0 + - - +
268A ASP 3.5 18.4 - - - -
269A LEU 3.4 12.0 - - - -
270A VAL* 1.3 81.8 + - - +
272A ILE* 1.3 70.0 + - - +
290A ILE* 5.9 0.4 - - + -
291A TYR 3.8 5.6 - - - -
292A SER* 2.5 35.0 + - - +
293A PHE* 4.6 0.7 - - - -
297A VAL* 3.8 11.1 - - + +
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Residues in contact with ILE 272 (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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106A MET* 4.3 19.3 - - + -
110A ARG* 4.9 0.4 - - - +
116A PHE* 4.3 13.7 - - + -
236A CYS 3.3 5.8 - - - +
238A GLU* 3.6 25.1 - - + +
252A SER* 3.9 7.0 - - - +
253A ILE* 3.5 31.4 - - + -
254A ALA* 4.1 13.7 - - + -
271A HIS* 1.3 78.2 - - - +
273A VAL* 1.3 77.7 + - - +
274A TYR* 4.4 2.9 - - + +
289A ILE 3.8 0.3 - - - +
290A ILE* 3.7 5.7 - - - +
291A TYR* 2.9 45.4 + - + +
293A PHE* 4.2 10.1 - - + -
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Residues in contact with VAL 273 (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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127A ALA* 4.3 7.2 - - + +
130A ALA* 3.6 26.5 - - + +
131A ASN* 3.4 27.8 - - - +
134A ILE* 4.1 17.0 - - + -
235A VAL* 3.7 26.9 - - + -
236A CYS 2.6 11.7 + - - +
237A ASP* 3.4 18.1 - - - +
238A GLU 3.0 26.3 + - - -
239A ILE 3.9 1.2 + - - -
272A ILE* 1.3 75.6 - - - +
274A TYR* 1.3 65.1 + - - +
289A ILE 3.6 3.6 - - - -
290A ILE* 5.1 2.5 - - + -
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Residues in contact with TYR 274 (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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102A ILE* 5.1 2.9 - - + -
105A PHE* 3.3 21.6 - + - -
106A MET* 4.0 38.1 - - + -
109A THR* 3.7 9.4 + - - -
110A ARG* 3.3 23.3 - - - -
127A ALA* 4.6 1.4 - - - -
238A GLU* 3.4 26.0 - - + -
239A ILE* 4.0 7.0 - - - +
241A ALA* 4.3 1.3 - - + -
272A ILE* 4.4 3.6 - - + -
273A VAL* 1.3 79.7 - - - +
275A SER* 1.3 92.1 + - - +
276A LEU* 4.3 11.2 - - + -
279A ASP* 2.8 26.9 + - - -
288A GLY* 3.7 1.2 - - - -
289A ILE* 2.8 47.9 + - + +
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Residues in contact with SER 275 (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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127A ALA* 4.0 9.0 - - - -
239A ILE* 3.7 28.7 - - - +
274A TYR* 1.3 105.5 - - - +
276A LEU* 1.3 72.2 + - - +
277A SER* 3.1 10.7 + - - -
279A ASP* 3.9 4.2 + - - +
287A VAL* 3.3 16.6 + - - -
289A ILE* 5.0 1.6 - - - -
500A PLP 3.0 23.7 + - - -
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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