Contacts of the strand formed by residues 251 - 256 (chain B) in PDB entry 3IXK
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 ILE 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B VAL* 5.1 0.2 - - + -
250B ILE* 1.3 73.3 - - - +
252B VAL* 1.3 63.8 + - - +
253B ARG 3.6 17.7 - - - +
254B VAL* 3.7 17.5 - - + -
265B CYS 4.1 5.0 - - - +
268B TYR* 4.0 13.2 - - + +
269B ASN* 2.8 33.3 + - - +
273B SER* 3.7 22.2 - - - +
284B LEU* 6.2 0.9 - - + -
333B LEU* 4.7 15.9 - - + -
334B TYR 3.3 13.5 - - - +
335B LEU* 3.8 19.5 - - + -
379B THR* 3.8 25.8 - - + +
381B MET* 4.5 10.3 - - - -
430B CYS* 4.1 1.4 - - - +
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Residues in contact with VAL 252 (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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250B ILE* 4.0 0.7 - - + -
251B ILE* 1.3 76.1 - - - +
253B ARG* 1.3 61.3 + - - +
265B CYS* 3.9 17.2 - - - +
334B TYR* 2.7 29.6 + - + +
335B LEU 4.2 6.5 - - - -
336B MET* 3.8 30.1 - - + -
424B THR* 3.3 36.5 - - + +
425B LEU* 3.4 32.3 + - - +
430B CYS* 3.9 17.9 - - - -
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Residues in contact with ARG 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ILE* 3.6 4.0 - - - +
252B VAL* 1.3 82.4 + - + +
254B VAL* 1.3 76.0 + - - +
255B GLU* 3.9 11.8 + - + -
260B ASP* 3.5 29.9 + - - +
268B TYR* 3.7 10.8 - - - -
334B TYR* 3.0 69.4 + - + -
422B PHE* 4.7 9.5 - - - -
423B VAL 3.8 20.1 + - - -
424B THR* 4.5 14.3 - - + +
425B LEU* 5.5 0.8 - - - +
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ILE* 3.7 18.6 - - + -
253B ARG* 1.3 84.5 - - - +
255B GLU* 1.3 75.4 + - - +
256B ILE* 4.7 3.1 - - + -
260B ASP* 3.6 2.6 - - - +
261B LEU* 2.8 48.0 + - + +
268B TYR* 3.8 32.8 + - + +
284B LEU* 6.6 0.2 - - + -
288B VAL* 5.3 3.8 - - + -
292B ALA* 6.3 0.4 - - + -
331B ILE* 4.5 7.4 - - + -
332B SER 3.2 9.2 - - - +
333B LEU* 3.8 19.3 - - + -
334B TYR* 4.6 0.2 - - - -
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Residues in contact with GLU 255 (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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253B ARG* 3.9 16.6 + - - -
254B VAL* 1.3 79.6 - - - +
256B ILE* 1.3 66.1 + - - +
258B GLY* 4.0 24.2 - - - +
259B GLN 3.3 8.1 - - - +
260B ASP* 3.7 21.9 + - + +
330B VAL 4.1 0.2 - - - +
331B ILE* 3.4 3.8 - - - +
332B SER* 2.6 49.8 + - - -
334B TYR* 2.8 33.5 + - + -
345B ARG* 4.0 8.0 + - - -
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Residues in contact with ILE 256 (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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254B VAL* 4.7 3.1 - - + -
255B GLU* 1.3 79.4 - - - +
257B ASN* 1.3 74.0 + - + +
258B GLY 3.1 0.2 - - - -
259B GLN* 3.1 25.8 + - + +
261B LEU* 3.8 28.7 - - + +
292B ALA* 3.9 31.0 - - + +
295B SER* 3.4 24.4 + - - +
296B ILE* 4.7 6.1 - - + -
329B PRO* 3.6 30.5 - - + -
330B VAL 3.5 4.0 - - - +
331B ILE* 4.1 20.0 - - + -
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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