Contacts of the strand formed by residues 350 - 354 (chain B) in PDB entry 1K8F
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 350 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B LYS* 2.9 17.3 + - + +
328B LYS* 3.7 29.6 - - + +
329B TRP* 2.7 34.6 + - - +
348B LYS 4.1 5.2 - - - +
349B GLN* 1.3 82.3 - - - +
351B ALA* 1.3 59.0 + - - +
352B TYR* 5.8 1.6 - - + -
367B ILE* 4.4 4.7 - - - -
368B ASN* 4.1 11.0 - - + +
369B SER* 3.2 28.7 - - - +
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B TRP* 3.6 16.2 - - + +
331B VAL* 5.3 2.0 - - + -
342B ILE* 5.4 0.2 - - + -
350B VAL* 1.3 78.2 - - - +
352B TYR* 1.3 61.8 + - - +
353B ILE* 4.0 5.6 - - + -
363B ILE* 3.8 29.8 - - + -
367B ILE* 4.1 9.1 - - + +
369B SER 2.9 7.5 + - - +
370B ILE* 3.4 11.3 - - + -
371B THR* 3.0 26.6 + - - -
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Residues in contact with TYR 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LYS* 3.9 34.1 - - + +
329B TRP 3.0 10.2 + - - -
330B ARG* 4.1 1.6 - - - -
331B VAL 3.2 22.3 + - - +
332B GLU* 4.6 4.6 - - - +
350B VAL* 4.4 1.3 + - + -
351B ALA* 1.3 73.4 - - - +
353B ILE* 1.3 65.7 + - - +
354B TYR* 3.4 24.6 + + + +
371B THR* 3.6 26.2 - - + +
373B ASP* 2.8 44.1 + - + +
392B ILE* 5.4 0.7 - - - +
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Residues in contact with ILE 353 (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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331B VAL* 3.1 25.6 - - + +
351B ALA* 4.5 5.6 - - + -
352B TYR* 1.3 71.6 - - - +
354B TYR* 1.3 57.3 + - - +
356B CYS* 3.7 17.3 - - - -
361B LEU* 3.9 24.5 - - + -
363B ILE* 4.7 0.2 - - + -
370B ILE* 3.5 32.3 - - + -
371B THR 2.9 9.3 + - - +
372B VAL* 4.1 15.3 - - + -
373B ASP* 2.9 28.4 + - - +
375B CYS* 3.4 7.2 - - - -
378B LEU* 3.5 34.3 - - + -
380B LEU* 4.4 5.6 - - + -
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Residues in contact with TYR 354 (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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331B VAL 3.0 7.1 + - - -
332B GLU* 3.0 47.2 - - + +
333B ASN* 3.0 2.8 + - - -
352B TYR* 3.4 18.8 + + + -
353B ILE* 1.3 74.1 - - - +
355B LYS* 1.3 110.0 + - + +
356B CYS* 3.0 5.3 + - - -
373B ASP* 3.2 36.8 - - + -
374B ASN* 3.8 19.1 + - + -
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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