Contacts of the strand formed by residues 357 - 367 (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 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334B GLN 3.1 6.3 + - - +
335B GLU* 3.6 30.1 - - + +
336B ASN* 3.3 10.7 + - - +
355B LYS 4.6 4.9 - - - +
356B CYS* 1.3 77.4 - - - +
358B ASN* 1.3 81.7 + - + +
359B THR* 3.0 9.3 + - - -
374B ASN 6.0 0.4 - - - +
376B LYS* 2.9 28.7 - - + +
377B LYS* 5.5 0.7 - - + -
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Residues in contact with ASN 358 (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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336B ASN* 2.7 40.6 + - - +
337B VAL 3.2 11.3 - - - +
357B VAL* 1.3 81.7 - - + +
359B THR* 1.3 58.0 + - - +
376B LYS 2.8 12.1 + - - -
377B LYS* 3.1 26.6 - - + +
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Residues in contact with THR 359 (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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334B GLN* 3.3 29.5 + - + +
335B GLU* 3.7 1.9 + - - -
336B ASN 4.1 0.9 + - - -
337B VAL* 3.2 10.1 + - + +
340B LEU* 3.4 31.9 - - + -
356B CYS* 4.2 12.1 - - + -
357B VAL* 3.0 14.4 + - - +
358B ASN* 1.3 77.2 - - - +
360B THR* 1.3 77.9 + - - +
361B LEU* 4.3 2.7 - - + +
377B LYS 3.3 3.7 + - - +
378B LEU* 3.4 13.8 - - + +
379B GLY 2.8 24.1 + - - -
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Residues in contact with THR 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B VAL 3.4 4.4 + - - -
338B SER* 3.0 34.5 - - - +
339B ASN 5.7 0.2 - - - -
340B LEU* 3.4 25.3 + - - +
359B THR* 1.3 78.9 + - - +
361B LEU* 1.3 65.7 + - - +
362B GLN* 6.2 0.7 - - + -
379B GLY* 3.2 17.0 + - - +
381B VAL* 5.6 4.9 - - + -
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Residues in contact with LEU 361 (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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322B LEU* 5.5 1.1 - - + -
331B VAL* 4.6 17.7 - - + -
340B LEU* 3.6 28.3 - - + +
341B VAL 4.1 2.0 - - - +
342B ILE* 4.2 16.2 - - + -
353B ILE* 3.9 22.2 - - + -
359B THR* 4.3 4.0 - - + -
360B THR* 1.3 76.5 - - - +
362B GLN* 1.3 91.3 + - - +
363B ILE* 3.6 30.1 - - + -
378B LEU* 5.6 5.8 - - + -
379B GLY 2.7 14.7 + - - +
380B LEU* 3.3 14.8 - - + +
381B VAL* 3.1 26.0 + - - +
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Residues in contact with GLN 362 (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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340B LEU 3.1 9.4 + - - +
341B VAL* 3.3 14.5 - - + +
342B ILE 2.9 24.6 + - - -
360B THR* 6.2 0.9 - - + -
361B LEU* 1.3 82.2 - - - +
363B ILE* 1.3 67.1 + - - +
364B LYS* 3.6 35.9 - - + +
381B VAL* 3.1 32.2 - - + +
383B ASP* 4.9 6.6 - - - +
402B MET* 5.8 1.2 - - - +
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Residues in contact with ILE 363 (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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329B TRP* 5.9 2.0 - - + -
342B ILE* 4.0 23.6 - - + -
345B THR* 4.1 17.0 - - - +
351B ALA* 3.8 22.2 - - + -
361B LEU* 3.6 26.2 - - + -
362B GLN* 1.3 78.9 - - - +
364B LYS* 1.3 64.4 + - - +
365B GLY 3.8 3.8 + - - +
367B ILE* 4.4 16.6 - - + -
370B ILE* 3.8 27.4 - - + -
380B LEU* 4.0 7.0 - - + -
381B VAL 3.0 7.5 + - - +
382B PHE* 3.4 8.9 - - + +
383B ASP* 3.4 25.3 + - - +
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Residues in contact with LYS 364 (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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341B VAL* 4.2 8.7 - - + -
342B ILE 3.1 9.9 + - - +
343B GLU* 2.9 54.8 + - - +
345B THR* 3.1 25.0 + - - -
362B GLN* 3.6 31.6 - - + +
363B ILE* 1.3 73.6 - - - +
365B GLY* 1.3 60.4 + - - +
383B ASP* 3.9 8.5 - - - +
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Residues in contact with GLY 365 (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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345B THR* 3.7 10.3 + - - -
363B ILE* 4.2 5.9 - - - +
364B LYS* 1.3 76.4 - - - +
366B LYS* 1.3 61.4 + - - -
367B ILE* 3.8 5.4 + - - +
382B PHE* 5.6 0.5 - - - +
383B ASP* 3.2 29.8 + - - +
384B ASP 3.5 8.8 + - - +
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Residues in contact with LYS 366 (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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345B THR* 3.7 6.7 - - - +
346B GLU 3.6 2.9 - - - +
347B LEU* 3.3 45.5 + - + +
365B GLY* 1.3 70.7 - - - -
367B ILE* 1.3 62.3 + - - +
384B ASP* 3.4 42.6 - - + +
385B VAL 4.8 1.8 + - - -
386B VAL* 3.5 27.3 - - + +
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Residues in contact with ILE 367 (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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329B TRP* 5.3 3.4 - - + -
345B THR* 3.6 24.5 - - + +
346B GLU 3.3 21.5 - - - +
347B LEU 3.7 4.9 - - - -
349B GLN* 3.5 16.2 - - + +
350B VAL* 4.4 1.3 - - - -
351B ALA* 4.1 17.0 - - + +
363B ILE* 4.4 13.9 - - + -
365B GLY 4.7 3.6 - - - +
366B LYS* 1.3 75.2 - - - +
368B ASN* 1.3 61.0 + - - +
369B SER 3.8 13.9 - - - +
370B ILE* 3.7 29.2 - - + -
382B PHE* 6.4 0.2 - - + -
384B ASP 3.3 10.0 + - - +
385B VAL* 3.3 10.1 - - + -
386B VAL* 2.9 25.3 + - - +
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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