Contacts of the strand formed by residues 335 - 346 (chain B) in PDB entry 1KP5
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 HIS 335 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332B VAL 2.7 47.8 + - - +
333B ASN* 3.3 12.5 + - + +
334B GLY* 1.3 70.5 - - - +
336B LYS* 1.3 61.7 + - - +
337B PHE* 3.5 8.9 - - - -
364B PRO* 3.8 25.1 - - + -
442B GLU* 3.4 34.9 + - - -
447B LEU* 4.6 9.1 - - + +
903B SO4 3.0 43.2 + - - +
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Residues in contact with LYS 336 (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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100A GLU* 6.2 2.3 - - - +
123A LYS* 4.0 31.6 - - + +
124A PHE 3.8 15.7 - - - +
125A GLU* 3.8 23.4 - - + +
126A GLY* 3.7 18.1 + - - +
330B GLY 3.3 6.7 - - - +
331B ASP* 3.6 32.3 + - + +
334B GLY* 3.2 12.2 + - - +
335B HIS* 1.3 74.6 - - - +
337B PHE* 1.3 66.3 + - - +
360B THR* 4.6 0.3 + - - -
364B PRO* 5.1 0.9 - - - +
903B SO4 4.2 6.1 + - - -
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Residues in contact with PHE 337 (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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125A GLU* 3.3 15.4 + - - +
328B LEU* 3.9 19.7 - - + -
329B ASP* 3.7 1.0 - - - +
330B GLY* 3.0 53.8 + - - +
332B VAL* 3.9 23.3 - - + -
335B HIS 3.5 9.2 - - - -
336B LYS* 1.3 76.5 - - - +
338B SER* 1.3 62.1 + - - +
339B VAL* 4.3 6.1 - - + -
358B CYS* 4.6 3.1 - - - -
360B THR* 3.3 14.8 - - - +
362B LYS 5.4 0.7 - - - +
363B LEU* 3.6 28.3 - - + -
364B PRO* 3.2 37.7 - - + -
365B VAL* 4.5 10.8 - - + -
370B LEU* 4.2 11.0 - - + -
435B LEU* 4.8 5.4 - - + -
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Residues in contact with SER 338 (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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25A LEU* 4.0 7.8 - - - +
27A GLU* 4.7 4.5 + - - +
125A GLU* 3.9 5.6 - - - -
132A ARG* 3.1 30.4 + - - -
327B GLU* 5.0 1.2 + - - -
328B LEU 3.3 7.6 + - - -
337B PHE* 1.3 78.6 - - - +
339B VAL* 1.3 74.0 + - - +
340B SER* 5.2 0.2 + - - -
358B CYS* 3.5 6.6 - - - -
359B THR* 3.2 36.7 + - - -
360B THR* 3.1 13.0 + - - -
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Residues in contact with VAL 339 (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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326B VAL* 3.8 1.2 - - + +
327B GLU* 3.6 6.1 - - - +
328B LEU* 2.9 35.1 + - + +
337B PHE* 4.3 8.1 - - + -
338B SER* 1.3 84.3 + - - +
340B SER* 1.3 73.6 + - - +
356B PHE* 3.9 15.5 - - + -
357B ILE 3.4 11.4 - - - +
358B CYS* 4.3 1.1 - - - -
359B THR* 4.6 0.7 - - - -
363B LEU* 3.8 28.5 - - + -
367B TRP* 4.1 8.3 - - + -
374B PHE* 3.5 37.9 - - + -
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Residues in contact with SER 340 (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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27A GLU* 3.3 13.2 + - - -
40A SER* 4.4 2.6 + - - -
325B LEU* 6.0 0.4 - - - -
326B VAL 3.3 3.6 - - - -
327B GLU* 2.5 30.3 + - - -
338B SER* 5.2 0.3 + - - -
339B VAL* 1.3 75.9 + - - +
341B GLY* 1.3 59.2 - - - +
355B LYS 3.9 0.5 - - - +
356B PHE* 3.3 0.7 - - - -
357B ILE* 2.8 35.4 + - - +
359B THR* 4.3 17.1 + - - +
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Residues in contact with GLY 341 (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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325B LEU* 3.6 6.4 - - - +
326B VAL* 2.8 39.8 + - - +
340B SER* 1.3 76.0 - - - +
342B GLU* 1.3 64.9 + - - +
354B LEU* 5.2 0.2 - - - -
355B LYS 3.0 12.8 - - - -
356B PHE* 3.7 18.1 - - - -
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Residues in contact with GLU 342 (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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59A THR* 5.0 10.7 - - - +
225A ARG* 4.4 19.5 + - - -
324B ILE 3.3 12.3 - - - +
325B LEU* 5.0 6.5 - - + +
341B GLY* 1.3 75.9 - - - +
343B GLY* 1.3 58.2 + - - +
354B LEU* 3.4 7.5 - - - +
355B LYS* 2.9 38.4 + - + +
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Residues in contact with GLY 343 (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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323B PRO* 3.6 4.9 - - - +
324B ILE* 2.8 27.3 + - - +
342B GLU* 1.3 78.3 - - - +
344B GLU* 1.3 66.6 + - - +
353B THR* 3.0 13.9 - - - -
354B LEU* 3.6 2.1 - - - +
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Residues in contact with GLU 344 (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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321B VAL* 3.6 29.6 - - + +
322B VAL 3.2 14.8 - - - +
323B PRO* 4.4 2.0 - - + -
324B ILE* 3.5 7.9 - - - +
343B GLY* 1.3 76.6 - - - +
345B GLY* 1.3 60.2 + - - +
351B LYS 4.1 0.7 - - - +
352B LEU* 3.8 0.5 - - - -
353B THR* 3.0 40.4 + - - +
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Residues in contact with GLY 345 (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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320B GLY 3.8 1.7 - - - +
321B VAL* 3.6 4.0 - - - -
322B VAL 2.9 33.5 + - - +
324B ILE* 3.4 3.0 - - - +
344B GLU* 1.3 75.2 - - - +
346B ASP* 1.3 60.7 + - - -
351B LYS 3.3 8.5 - - - -
352B LEU* 3.8 7.2 - - - -
381B PHE* 3.5 27.1 - - - -
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Residues in contact with ASP 346 (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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319B THR 4.8 0.3 - - - +
320B GLY* 3.9 16.6 - - - +
321B VAL* 4.2 20.5 - - + +
345B GLY* 1.3 72.4 - - - +
347B ALA* 1.3 62.3 + - - +
348B THR* 4.0 9.4 + - - -
349B TYR* 3.0 36.2 + - - +
350B GLY 2.9 21.0 + - - -
351B LYS* 2.8 29.5 + - + +
381B PHE* 4.1 1.0 - - - -
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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