Contacts of the helix formed by residues 334 - 355 (chain B) in PDB entry 5KJH
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 SER 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B ASP* 2.7 39.2 + - - +
332B PRO 4.7 0.4 - - - -
333B ASN* 1.3 76.4 - - - +
335B ALA* 1.3 64.1 + - - +
336B GLU* 3.5 13.5 + - - -
337B GLU* 3.2 15.1 + - - +
338B GLN* 3.2 31.1 + - - +
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B SER* 1.3 72.8 - - - +
336B GLU* 1.4 65.3 + - - +
338B GLN* 3.4 11.5 + - - +
339B LYS* 3.0 28.6 + - - +
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Residues in contact with GLU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ARG* 5.6 6.1 - - - +
329B ASP 5.7 0.2 - - - +
330B VAL* 3.8 16.6 - - + -
331B ASP* 5.4 0.6 - - - +
334B SER* 3.3 13.4 + - - +
335B ALA* 1.4 83.5 + - - +
337B GLU* 1.4 59.2 + - - +
339B LYS* 3.4 2.9 + - + -
340B TYR* 2.9 26.2 + - - +
847B PHE* 3.3 35.8 - - + -
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B VAL* 3.7 27.4 - - + +
331B ASP 3.4 14.4 - - - +
332B PRO* 3.3 20.6 - - - +
333B ASN* 2.8 29.1 + - - -
334B SER* 3.2 14.7 + - - +
336B GLU* 1.4 75.1 - - - +
338B GLN* 1.4 54.4 + - + +
340B TYR* 3.4 3.9 + - + +
341B SER* 2.8 37.9 + - - +
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Residues in contact with GLN 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ASN* 5.8 1.8 - - - +
334B SER 3.2 21.4 + - - +
335B ALA* 3.5 11.8 - - - +
337B GLU* 1.4 76.5 - - + +
339B LYS* 1.4 58.6 + - - +
341B SER* 3.4 9.2 + - - +
342B ALA* 3.0 30.5 + - - +
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Residues in contact with LYS 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ALA 3.0 18.3 + - - +
336B GLU* 3.4 7.2 + - + +
338B GLN* 1.4 73.5 - - - +
340B TYR* 1.4 62.5 + - - +
342B ALA* 3.4 7.0 + - - +
343B TRP* 3.1 22.7 + - - +
846B VAL* 2.9 38.5 + - + +
847B PHE* 3.7 28.0 - - + +
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Residues in contact with TYR 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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324B VAL* 3.3 22.4 - - + +
325B PRO 3.0 29.9 + - - -
326B HIS* 4.0 15.2 - + - -
327B LEU* 4.4 18.8 - - + -
328B ARG 5.8 3.4 - - - -
330B VAL* 4.2 23.8 - - + -
336B GLU 2.9 18.8 + - - +
337B GLU* 3.6 4.3 - - + +
339B LYS* 1.4 76.1 - - - +
341B SER* 1.4 60.0 + - - +
343B TRP* 3.3 19.4 + + - +
344B LEU* 3.1 50.1 + - + +
846B VAL* 4.6 1.3 - - - -
847B PHE* 3.9 15.8 - + + -
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLU* 2.8 24.0 + - - +
338B GLN* 3.4 13.7 + - - +
340B TYR* 1.4 76.1 - - - +
342B ALA* 1.4 58.2 + - - +
344B LEU* 3.6 12.8 + - - +
345B MET* 3.1 33.1 + - - +
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Residues in contact with ALA 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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338B GLN 3.0 18.9 + - - +
339B LYS* 3.6 7.4 - - - +
340B TYR 3.3 0.2 - - - -
341B SER* 1.4 73.4 + - - +
343B TRP* 1.4 59.0 + - - +
345B MET* 3.3 7.7 + - - +
346B ASP* 2.9 38.0 + - - +
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Residues in contact with TRP 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B PRO* 3.5 43.3 - - + -
327B LEU* 3.8 27.6 - - + -
339B LYS 3.1 13.0 + - - +
340B TYR* 3.3 13.2 + + - +
342B ALA* 1.4 71.2 - - - +
344B LEU* 1.4 84.3 + - + +
346B ASP* 3.4 13.0 + - + +
347B LEU* 3.0 47.7 + - + +
841B HIS* 3.2 33.0 + - + +
842B ARG 4.1 4.0 - - - -
844B GLY* 3.6 20.5 - - - -
845B ASP 5.1 0.2 - - - +
846B VAL* 3.3 35.9 - - + +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LEU* 5.8 0.4 - - + -
324B VAL* 4.1 11.7 - - + -
325B PRO* 3.8 21.5 - - + -
340B TYR* 3.1 51.5 + - + +
341B SER* 3.8 11.7 - - - +
342B ALA 3.4 0.4 - - - -
343B TRP* 1.4 100.2 - - + +
345B MET* 1.3 60.7 + - + +
347B LEU* 3.4 10.5 + - + +
348B GLU* 3.1 27.5 + - - +
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Residues in contact with MET 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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341B SER* 3.1 21.5 + - - +
342B ALA* 3.5 9.2 - - - +
343B TRP 3.3 0.2 - - - -
344B LEU* 1.3 77.9 - - + +
346B ASP* 1.4 51.6 + - - +
348B GLU* 3.1 42.6 + - - +
349B ASN* 2.8 56.7 + - - +
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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
----------------------------------------------------------
342B ALA* 2.9 25.7 + - - +
343B TRP* 3.4 12.5 + - + +
345B MET* 1.4 77.6 - - - +
347B LEU* 1.4 61.4 + - + +
349B ASN* 3.1 11.9 + - - +
350B LEU* 3.1 28.6 + - + +
841B HIS* 5.7 5.6 - - + +
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LEU* 3.8 31.3 - - + +
325B PRO* 4.0 6.1 - - + -
343B TRP* 3.0 60.4 + - + +
344B LEU* 3.4 13.5 - - + +
346B ASP* 1.4 73.7 - - + +
348B GLU* 1.4 62.4 + - - +
350B LEU* 3.3 20.2 + - + +
351B ASP* 3.4 17.6 + - - +
841B HIS* 3.5 44.6 - - + +
842B ARG* 3.9 9.2 - - + +
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Residues in contact with GLU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LEU* 5.6 0.8 - - - +
344B LEU 3.1 12.8 + - - +
345B MET* 3.1 44.1 + - - +
347B LEU* 1.4 74.8 - - - +
349B ASN* 1.4 58.1 + - - +
351B ASP* 3.4 9.6 + - + +
352B SER* 3.2 27.4 + - - -
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Residues in contact with ASN 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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345B MET* 2.8 44.0 + - - +
346B ASP* 3.1 14.9 + - - +
348B GLU* 1.4 77.5 + - - +
350B LEU* 1.3 58.3 + - - +
352B SER* 2.9 21.7 + - - -
353B LYS* 3.2 18.2 - - - +
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Residues in contact with LEU 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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346B ASP 3.1 18.9 + - - +
347B LEU* 3.5 14.6 - - + +
348B GLU 3.3 0.4 - - - -
349B ASN* 1.3 75.4 - - + +
351B ASP* 1.4 61.2 + - - +
353B LYS* 3.5 17.2 + - + +
354B SER* 2.9 26.9 + - - -
837B VAL* 3.8 26.7 - - + +
838B ARG* 4.3 21.8 - - + +
841B HIS* 3.5 40.6 - - + +
2530B GLU* 4.2 19.5 - - + -
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Residues in contact with ASP 351 (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 GLN* 3.3 28.7 + - + +
321B LEU* 3.1 37.0 + - - +
347B LEU 3.4 12.0 + - - +
348B GLU* 3.4 10.5 + - + +
350B LEU* 1.4 75.2 - - - +
352B SER* 1.4 63.8 + - - +
354B SER* 2.7 26.0 + - - +
355B GLY 3.6 2.8 + - - -
356B PHE* 4.3 6.6 + - + +
838B ARG* 4.0 19.2 - - - +
842B ARG* 5.8 0.5 + - - -
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLU* 3.2 10.6 + - - -
349B ASN* 2.9 29.8 + - - -
351B ASP* 1.4 75.6 - - - +
353B LYS* 1.4 58.1 + - - +
354B SER 3.5 0.7 + - - -
355B GLY* 3.8 9.2 + - - -
356B PHE 5.3 0.2 + - - -
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Residues in contact with LYS 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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349B ASN 3.2 17.2 + - - +
350B LEU* 3.5 16.4 - - + +
352B SER* 1.4 76.7 + - - +
354B SER* 1.3 58.3 + - - +
355B GLY 3.4 0.4 - - - -
523B ARG* 3.0 20.8 + - - -
834B ASP* 4.9 20.0 + - - +
837B VAL* 6.1 0.4 - - - +
2530B GLU* 3.5 42.8 + - + +
2531B VAL* 5.8 1.0 - - - +
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Residues in contact with SER 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B GLN* 6.1 0.5 - - - +
350B LEU 2.9 14.6 + - - -
351B ASP* 2.7 23.6 + - - +
353B LYS* 1.3 78.3 - - - +
355B GLY* 1.3 60.5 + - - +
356B PHE* 3.7 17.0 - - - +
523B ARG* 3.3 29.0 + - - +
834B ASP* 5.7 4.9 - - - -
838B ARG* 4.2 30.8 + - - +
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Residues in contact with GLY 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B ASP 3.6 3.0 + - - -
352B SER 3.8 7.1 + - - -
353B LYS 3.4 2.6 - - - -
354B SER* 1.3 81.0 + - - +
356B PHE* 1.4 62.5 + - - +
523B ARG* 3.8 29.9 - - - +
524B ASP* 4.6 4.7 + - - +
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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
------------------------------------------------------------
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