Contacts of the strand formed by residues 346 - 350 (chain B) in PDB entry 1K3B
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 MET 346 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242B MET* 3.6 6.5 - - - -
246B ARG* 4.1 9.6 - - - +
324B VAL* 4.2 4.9 - - - -
336B MET* 3.5 14.6 - - - +
339B GLU* 3.6 16.2 - - + -
340B LEU* 3.4 46.0 - - + +
344B GLY 3.5 4.7 + - - +
345B PRO* 1.3 76.0 - - - +
347B ALA* 1.3 70.9 + - - +
348B VAL* 4.2 4.3 - - + -
384C LEU* 3.3 6.3 - - - +
385C LEU* 2.9 42.9 + - + +
430C ALA* 3.8 21.8 - - + -
431C VAL 3.2 14.4 - - - +
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Residues in contact with ALA 347 (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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238B ALA* 4.3 13.0 - - + +
242B MET* 3.7 14.1 - - + -
279B PRO* 3.6 35.0 - - + -
346B MET* 1.3 72.6 - - - +
348B VAL* 1.3 59.3 + - - +
383C VAL 3.4 10.1 - - - +
384C LEU* 4.1 3.1 - - - +
429C ILE 3.9 1.2 - - - +
430C ALA* 3.2 3.5 - - - -
431C VAL* 2.7 41.4 + - + +
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Residues in contact with VAL 348 (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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279B PRO* 6.0 1.1 - - - -
336B MET* 3.9 18.8 - - + -
346B MET* 4.2 2.7 - - + -
347B ALA* 1.3 80.3 - - - +
349B ALA* 1.3 61.5 + - - +
382C ALA* 3.4 5.1 - - - +
383C VAL* 2.8 57.2 + - + +
385C LEU* 4.0 24.9 - - + +
401C VAL* 4.7 1.8 - - + -
426C ILE* 4.0 27.8 - - + +
429C ILE 4.1 8.1 - - - -
430C ALA* 3.8 19.5 - - + +
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Residues in contact with ALA 349 (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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278B PHE* 6.4 2.5 - - + -
279B PRO* 6.1 3.1 - - + -
348B VAL* 1.3 77.5 - - - +
350B PHE* 1.3 64.0 + - - +
379C THR* 3.8 17.0 - - - +
381C HIS 3.2 13.0 - - - +
382C ALA* 4.3 7.9 - - + -
425C ALA 3.0 20.3 - - - +
426C ILE* 3.5 7.4 + - - -
429C ILE* 3.5 28.1 - - + +
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Residues in contact with PHE 350 (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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349B ALA* 1.3 76.9 - - - +
351B GLU* 1.3 78.6 + - - +
352B VAL* 3.3 30.2 + - + -
356B PHE* 3.6 37.0 - + + -
364B TYR* 5.4 1.1 - + - -
379C THR* 3.8 10.1 - - - -
380C ASN* 2.9 20.1 + - - +
381C HIS* 3.1 40.7 + - - +
383C VAL* 3.8 24.7 - - + -
415C PHE* 3.8 9.6 - + - -
417C ILE* 4.7 8.7 - - + -
424C CYS* 3.2 22.7 - - + +
426C ILE* 3.9 22.9 - - + -
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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