Contacts of the strand formed by residues 331 - 335 (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 331 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B VAL* 4.5 4.7 - - + -
255B GLU 3.4 7.9 - - - +
256B ILE* 4.1 21.1 - - + -
282B LEU* 5.0 9.0 - - + -
292B ALA* 5.8 2.7 - - + -
296B ILE* 4.2 13.2 - - + -
329B PRO* 4.4 2.2 - - + +
330B VAL* 1.3 79.3 - - - +
332B SER* 1.3 66.8 - - - +
333B LEU* 4.1 21.3 + - + -
346B ILE 3.5 1.6 - - - +
347B THR* 3.3 4.1 - - - -
348B ILE* 2.9 46.0 + - + +
353B TYR* 3.9 26.9 - - + +
372B ILE* 3.9 22.0 - - + -
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Residues in contact with SER 332 (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* 3.2 9.5 - - - +
255B GLU* 2.6 57.4 + - - +
330B VAL* 5.6 1.6 - - - +
331B ILE* 1.3 73.0 - - - +
333B LEU* 1.3 63.2 - - - +
334B TYR* 3.8 14.4 + - - -
345B ARG* 3.7 14.5 + - - -
346B ILE 3.5 2.9 - - - -
347B THR* 3.3 24.9 + - - +
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Residues in contact with LEU 333 (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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251B ILE* 4.7 19.1 - - + -
253B ARG 4.0 1.6 - - - -
254B VAL* 3.8 30.3 - - + -
282B LEU* 4.4 18.8 - - + -
284B LEU* 5.7 5.6 - - + -
331B ILE* 4.1 12.5 + - + +
332B SER* 1.3 74.8 - - - +
334B TYR* 1.3 64.2 + - - +
335B LEU* 3.7 4.8 + - + +
345B ARG* 3.2 1.2 - - - -
346B ILE* 2.9 52.7 + - + +
348B ILE* 5.8 1.3 - - + -
379B THR* 5.8 0.2 - - + -
381B MET* 4.5 16.6 - - + -
385B ILE* 4.0 27.6 - - + -
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Residues in contact with TYR 334 (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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251B ILE* 3.3 8.3 - - - +
252B VAL* 2.7 45.7 + - + -
253B ARG* 3.0 52.0 + - + +
255B GLU* 2.8 35.1 + - + -
332B SER* 3.9 17.5 - - - -
333B LEU* 1.3 74.4 - - - +
335B LEU* 1.3 57.3 + - - +
344B PHE 3.2 8.5 - - - +
345B ARG* 3.0 38.4 + - + -
422B PHE* 3.8 40.4 - + + -
424B THR* 4.6 4.0 - - + -
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Residues in contact with LEU 335 (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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239B THR* 3.9 11.7 - - + +
249B VAL* 4.0 19.7 - - + -
250B ILE 3.7 7.9 - - - +
251B ILE* 3.8 27.4 - - + -
252B VAL* 4.2 3.1 - - - -
333B LEU* 4.4 7.0 - - + +
334B TYR* 1.3 75.1 - - - +
336B MET* 1.3 66.2 + - - +
337B GLY 3.3 2.6 + - - -
343B SER* 3.4 3.8 - - - -
344B PHE* 2.9 45.0 + - + -
346B ILE* 4.0 17.9 - - + -
381B MET* 4.4 7.4 - - + -
402B PHE* 3.6 36.3 - - + -
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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