Contacts of the helix formed by residues 404 - 417 (chain B) in PDB entry 4KJQ
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 ALA 404 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B PHE* 4.5 9.4 - - + -
202B GLU* 3.1 23.3 - - - +
203B GLU* 4.3 10.3 - - + +
357B PHE* 6.1 1.1 - - + -
398B LEU* 3.7 8.0 + - + +
399B ALA* 4.5 3.1 + - - -
402B ILE* 3.3 16.8 - - + -
403B ARG* 1.3 79.8 - - - +
405B PRO* 1.3 60.9 - - - +
406B LEU 3.2 0.3 + - - -
407B THR* 3.3 9.1 + - - -
408B GLY* 2.9 24.6 + - - -
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Residues in contact with PRO 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A ILE* 5.9 2.7 - - + -
216A LYS* 6.0 6.3 - - + -
219A PHE* 4.7 16.6 - - + -
202B GLU* 3.0 9.9 - - - +
395B GLY 5.7 0.2 - - - +
399B ALA* 3.9 19.7 - - + -
403B ARG* 3.5 8.7 - - - +
404B ALA* 1.3 87.3 - - - +
406B LEU* 1.3 57.6 + - - +
408B GLY* 4.5 1.6 - - - +
409B ILE* 3.0 41.4 + - + +
429B GLY 4.3 8.5 - - - +
430B LEU* 5.1 2.9 - - + +
433B THR* 3.6 31.4 - - + +
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Residues in contact with LEU 406 (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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194A LEU* 4.6 12.3 - - + -
197A ILE* 4.3 14.4 - - + -
198A LEU* 3.9 14.4 - - + -
201A ILE* 3.9 16.4 - - + -
215A ILE* 5.1 4.3 - - + -
219A PHE* 3.5 32.7 - - + -
198B LEU* 3.6 30.1 - - + -
202B GLU* 3.1 22.1 + - + +
405B PRO* 1.3 81.5 - - - +
407B THR* 1.3 57.1 + - - +
409B ILE* 3.9 2.3 - - + +
410B ILE* 3.0 44.9 + - + +
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Residues in contact with THR 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 4.8 1.6 - - + -
195B ALA* 3.8 18.0 - - + +
198B LEU* 3.4 12.1 - - - +
199B PHE* 3.3 55.8 + - + -
202B GLU* 2.7 23.1 + - - +
357B PHE* 4.6 12.6 - - + -
404B ALA* 3.3 4.9 + - - -
406B LEU* 1.3 74.3 - - - +
408B GLY* 1.3 60.5 + - - +
410B ILE* 4.3 1.5 - - - +
411B LEU* 2.8 34.1 + - + +
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Residues in contact with GLY 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B PHE* 5.7 0.2 - - - -
395B GLY* 4.4 12.6 - - - -
398B LEU* 4.0 25.7 - - - +
404B ALA 2.9 15.2 + - - -
405B PRO 3.8 2.0 - - - -
407B THR* 1.3 75.2 - - - +
409B ILE* 1.3 62.8 + - - +
411B LEU* 3.0 4.3 + - - +
412B VAL* 2.9 29.8 + - - +
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Residues in contact with ILE 409 (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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194A LEU* 4.6 8.5 - - + -
219A PHE* 4.2 15.9 - - + -
395B GLY* 5.1 4.4 + - - +
399B ALA* 6.5 0.2 - - + -
405B PRO* 3.0 26.3 + - + +
406B LEU* 3.9 3.4 - - + +
408B GLY* 1.3 72.4 - - - +
410B ILE* 1.3 59.9 + - - +
412B VAL* 3.3 6.0 + - - +
413B LEU* 2.8 27.6 + - + +
422B ILE* 4.0 26.2 - - + -
425B MET* 3.7 27.2 - - + +
426B ILE* 3.5 41.1 - - + +
429B GLY* 4.7 9.4 - - - -
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Residues in contact with ILE 410 (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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194A LEU* 3.8 26.0 - - + -
198A LEU* 4.4 4.0 - - + -
410A ILE* 3.9 25.4 - - + -
194B LEU* 3.8 32.8 - - + -
195B ALA* 4.1 7.4 - - - +
198B LEU* 3.9 20.6 - - + -
406B LEU* 3.0 36.0 + - + +
407B THR* 4.3 3.1 - - - +
409B ILE* 1.3 71.7 - - + +
411B LEU* 1.3 61.2 + - - +
413B LEU* 3.8 10.3 - - + +
414B GLU* 3.0 26.9 + - + +
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 5.8 0.7 - - + -
190B PHE* 3.7 25.4 - - + -
192B ALA* 3.7 25.1 - - + -
195B ALA* 3.9 14.1 - - + +
357B PHE* 3.5 31.9 - - + -
361B LEU* 4.0 18.4 - - + -
398B LEU* 4.2 4.7 - - + -
407B THR* 2.8 22.5 + - + +
408B GLY 3.0 2.9 + - - +
410B ILE* 1.3 75.4 - - - +
412B VAL* 1.3 66.5 + - - +
414B GLU* 2.9 13.7 + - - +
415B MET* 3.0 36.1 + - + +
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 4.4 7.4 - - + -
391B ILE* 3.7 23.6 - - + +
394B MET* 3.3 43.3 - - + +
395B GLY* 3.6 17.9 - - - +
408B GLY 2.9 18.4 + - - +
409B ILE* 3.8 3.8 - - - +
411B LEU* 1.3 74.2 - - + +
413B LEU* 1.3 55.5 + - - +
415B MET* 4.9 0.4 - - + -
416B THR* 2.6 50.3 + - - +
425B MET* 4.0 13.5 - - - -
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Residues in contact with LEU 413 (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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194A LEU* 4.5 17.7 - - + -
413A LEU* 4.1 26.5 - - + -
414A GLU* 6.3 0.4 - - + -
419A TYR* 5.1 5.4 - - + -
194B LEU* 6.0 0.4 - - + -
409B ILE 2.8 18.1 + - - +
410B ILE* 3.8 11.7 - - + +
412B VAL* 1.3 77.0 - - - +
414B GLU* 1.3 62.3 + - + +
416B THR* 4.5 2.2 - - - -
417B ASP* 3.0 29.3 + - - +
418B ASN 4.4 3.8 - - - +
419B TYR* 3.6 55.2 - - + +
422B ILE* 4.7 1.8 - - + -
425B MET* 4.3 16.1 - - + -
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Residues in contact with GLU 414 (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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419A TYR* 2.7 55.0 + - + +
191B ASN 4.5 5.0 - - - +
192B ALA* 3.4 20.0 - - + +
193B PRO* 3.2 7.6 - - - +
194B LEU* 2.9 40.3 + - + +
195B ALA* 2.7 32.1 + - - +
410B ILE* 3.0 17.0 + - + +
411B LEU 2.9 6.7 + - - +
413B LEU* 1.3 79.2 - - + +
415B MET* 1.3 61.5 + - - +
417B ASP* 4.8 0.8 - - - +
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Residues in contact with MET 415 (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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190B PHE* 3.7 43.3 - - - +
192B ALA* 5.1 0.2 - - + -
237B ALA* 5.7 1.2 - - - +
238B LEU* 5.3 7.4 - - + -
239B ILE* 3.2 42.3 - - + +
317B PHE* 5.0 3.1 - - - -
361B LEU* 3.8 20.6 - - + -
394B MET* 3.6 27.6 - - + -
411B LEU* 3.0 37.2 + - + +
412B VAL* 4.0 1.8 - - - +
414B GLU* 1.3 83.1 - - + +
416B THR* 1.3 60.5 + - - +
417B ASP* 3.6 1.0 - - - +
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Residues in contact with THR 416 (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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239B ILE* 4.0 19.5 - - + -
241B VAL* 3.9 13.8 + - + +
242B GLY 4.3 1.4 + - - +
320B ILE* 5.6 0.2 - - + -
391B ILE* 3.6 34.2 - - + +
394B MET* 3.7 25.4 - - + -
412B VAL* 2.6 39.6 + - - +
413B LEU* 4.5 1.0 - - - -
415B MET* 1.3 76.2 - - - +
417B ASP* 1.3 57.5 + - - +
418B ASN* 2.6 29.3 + - - -
425B MET* 5.3 0.7 - - - -
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Residues in contact with ASP 417 (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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243A LYS* 4.2 15.7 + - - -
417A ASP* 4.0 14.9 - - - +
419A TYR* 3.9 34.7 + - + +
420A GLN* 4.9 1.9 + - - +
242B GLY 4.8 0.5 - - - +
243B LYS* 3.7 15.8 + - - -
413B LEU* 3.0 19.3 + - - +
414B GLU 4.8 0.6 - - - +
415B MET 3.6 2.1 - - - +
416B THR* 1.3 77.9 + - - +
418B ASN* 1.3 62.8 + - - +
419B TYR* 3.7 4.2 + - - +
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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