Contacts of the strand formed by residues 270 - 275 (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 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B LEU* 3.9 25.6 - - + -
234B LEU* 3.7 6.7 - - + +
253B ILE* 4.2 23.3 - - + -
257B LEU* 3.6 36.8 - - + -
265B CYS* 5.9 0.4 - - + -
266B ASN 3.7 15.7 - - - +
267B LYS* 3.7 6.9 + - - +
268B ASP 3.3 4.0 - - - -
269B LEU* 1.3 82.8 - - - +
271B HIS* 1.3 66.9 + - - +
293B PHE* 3.0 40.5 + - + +
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Residues in contact with HIS 271 (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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134B ILE* 3.9 21.8 - - + -
138B LEU* 3.2 21.5 - - + +
233B HIS* 2.7 38.4 - + + -
234B LEU 3.1 9.4 + - - +
235B VAL* 3.4 9.5 - - + -
236B CYS* 2.8 28.6 + - - +
268B ASP 3.3 21.7 + - - -
269B LEU 3.9 1.0 - - - -
270B VAL* 1.3 78.7 + - - +
272B ILE* 1.3 66.0 + - - +
291B TYR 3.9 4.7 - - - -
292B SER* 2.6 29.1 + - - +
293B PHE* 4.6 0.4 - - - -
294B ASN* 4.0 1.1 - - + -
297B VAL* 3.6 20.1 - - + +
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Residues in contact with ILE 272 (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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106B MET* 4.3 16.8 - - + -
110B ARG* 4.6 0.4 - - - +
116B PHE* 4.0 26.9 - - + -
236B CYS 3.4 7.2 - - - +
238B GLU* 3.7 28.0 - - + +
252B SER* 4.1 5.4 - - - +
253B ILE* 3.6 30.5 - - + -
254B ALA* 4.2 2.2 - - + -
271B HIS* 1.3 74.6 - - - +
273B VAL* 1.3 79.1 + - - +
274B TYR* 4.8 1.3 - - + -
290B ILE* 3.8 4.2 - - - +
291B TYR* 3.0 41.4 + - + +
293B PHE* 4.1 15.0 - - + -
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Residues in contact with VAL 273 (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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127B ALA* 4.6 6.3 - - + +
130B ALA* 3.8 31.6 - - + +
131B ASN* 3.3 29.6 - - - +
134B ILE* 4.4 10.5 - - + -
235B VAL* 4.2 19.1 - - + -
236B CYS 2.7 13.2 + - - +
237B ASP* 3.8 17.2 - - - +
238B GLU 3.2 23.6 + - - -
239B ILE 3.9 1.9 + - - -
272B ILE* 1.3 80.1 - - - +
274B TYR* 1.3 70.4 - - - +
289B ILE 3.7 2.9 - - - +
290B ILE* 4.9 2.7 - - + -
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Residues in contact with TYR 274 (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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102B ILE* 4.9 2.9 - - + -
105B PHE* 3.0 23.2 - + - -
106B MET* 4.0 37.7 - - + -
109B THR* 4.1 5.5 + - - -
110B ARG* 3.7 19.3 - - - -
127B ALA* 4.5 2.1 - - - -
238B GLU* 3.5 26.9 - - + -
239B ILE* 4.1 9.4 - - - -
241B ALA* 4.5 0.7 - - + -
272B ILE* 4.8 2.2 - - + -
273B VAL* 1.3 81.6 - - - +
275B SER* 1.3 87.3 + - - +
276B LEU* 4.0 13.7 - - + -
279B ASP* 2.9 30.1 + - - -
288B GLY* 3.6 2.1 - - - -
289B ILE* 2.7 53.8 + - + +
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Residues in contact with SER 275 (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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127B ALA 4.0 5.4 - - - -
239B ILE* 3.5 31.3 - - - +
274B TYR* 1.3 105.3 - - - +
276B LEU* 1.3 71.7 + - - +
277B SER* 2.8 24.2 + - - -
279B ASP* 4.0 3.3 - - - +
287B VAL 3.0 19.4 + - - -
289B ILE* 4.6 0.7 - - - +
501B PLP 3.0 10.4 + - - -
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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