Contacts of the helix formed by residues 403 - 421 (chain B) in PDB entry 4D1Q
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 403 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ASN* 5.3 3.4 - - - +
355B SER* 4.4 17.7 - - - +
356B ILE* 4.8 12.6 - - + -
359B THR* 5.9 1.3 - - - +
401B GLY 4.0 8.1 - - - +
402B ASP* 1.3 70.5 - - - +
404B ALA* 1.3 59.4 + - + +
405B ASP* 2.7 27.9 + - + +
406B ILE* 2.9 32.7 + - + +
407B ALA* 2.9 9.1 + - - -
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ASP 3.6 3.0 + - - -
403B VAL* 1.3 74.4 - - + +
405B ASP* 1.3 64.0 + - - +
407B ALA* 3.6 9.9 - - - +
408B LYS* 3.1 24.1 + - - +
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Residues in contact with ASP 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B THR* 4.3 4.7 - - - +
283B GLU* 3.5 47.3 - - + +
284B LEU* 4.7 7.4 - - + +
287B PRO* 6.0 0.3 - - - +
356B ILE* 3.9 28.4 - - + +
403B VAL* 2.7 11.4 + - + +
404B ALA* 1.3 74.7 - - - +
406B ILE* 1.3 57.7 + - - +
408B LYS* 2.8 27.1 + - - +
409B LEU* 2.9 11.7 + - - +
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Residues in contact with ILE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LEU* 4.9 2.9 - - + -
356B ILE* 4.0 28.7 - - + -
359B THR* 3.5 39.5 - - + -
360B MET* 4.3 13.0 - - + +
363B ILE* 4.6 3.4 - - + -
402B ASP* 4.6 9.9 - - - +
403B VAL* 2.9 28.0 + - + +
405B ASP* 1.3 75.9 - - - +
407B ALA* 1.3 66.5 + - - +
409B LEU* 3.0 14.5 + - + +
410B LYS* 2.9 45.3 + - + +
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ASP* 4.3 21.5 - - + +
403B VAL 2.9 13.9 + - - +
404B ALA* 3.6 11.9 - - - +
406B ILE* 1.3 85.2 - - - +
408B LYS* 1.3 59.7 + - - +
410B LYS* 3.4 6.0 + - - +
411B VAL* 2.9 32.3 + - + +
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Residues in contact with LYS 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLU 5.2 2.9 - - - +
281B THR* 4.6 5.6 - - + -
282B PRO* 5.9 0.2 - - + -
283B GLU* 3.0 38.0 + - - +
404B ALA 3.1 13.7 + - - +
405B ASP* 2.8 14.4 + - - +
407B ALA* 1.3 77.8 - - - +
409B LEU* 1.3 62.3 + - - +
411B VAL* 3.2 12.3 + - + +
412B ASN* 3.1 33.4 + - - +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B SER* 4.8 0.9 - - - -
278B PHE* 4.5 23.8 - - + +
281B THR* 3.8 21.9 - - + +
284B LEU* 3.9 28.3 - - + -
360B MET* 4.4 17.7 - - + -
363B ILE* 4.5 20.2 - - + -
364B LEU* 6.3 1.6 - - + -
405B ASP 2.9 8.9 + - - +
406B ILE* 3.1 16.2 - - + +
408B LYS* 1.3 75.9 - - - +
410B LYS* 1.3 54.9 + - - +
412B ASN* 2.8 23.7 + - - +
413B ILE* 2.9 41.6 + - + +
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Residues in contact with LYS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B THR* 5.6 1.8 - - - +
363B ILE* 3.9 30.5 - - + +
395B ILE 3.6 10.8 + - - -
396B CYS* 3.8 41.9 - - + +
397B SER 3.4 17.0 + - - +
398B PRO* 4.8 1.3 - - + -
399B ASP* 3.5 17.8 + - - -
402B ASP* 3.6 28.8 + - - +
406B ILE* 2.9 29.6 + - - +
407B ALA* 3.5 7.2 - - - +
408B LYS 3.4 0.2 - - - -
409B LEU* 1.3 72.3 - - - +
411B VAL* 1.3 66.0 + - + +
412B ASN 3.0 0.5 + - - -
413B ILE* 3.0 4.6 + - - +
414B ILE* 2.9 26.7 + - - +
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B ALA* 2.9 21.1 + - + +
408B LYS* 3.4 10.5 - - + +
410B LYS* 1.3 76.1 - - + +
412B ASN* 1.3 63.5 - - - +
414B ILE* 3.7 8.8 + - - +
415B LYS* 3.1 25.8 + - + +
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Residues in contact with ASN 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B SER* 3.7 9.6 - - - +
280B GLU* 2.8 35.5 + - - +
281B THR* 3.2 13.2 + - - +
408B LYS* 3.1 20.4 + - - +
409B LEU 2.8 9.8 + - - +
411B VAL* 1.3 85.0 - - - +
413B ILE* 1.3 65.7 + - - +
415B LYS* 3.1 30.3 + - - +
416B ASN* 2.9 28.9 + - - +
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Residues in contact with ILE 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 4.3 3.0 - - + +
274B LEU* 5.0 7.9 - - + -
277B SER* 3.1 25.3 + - - +
278B PHE* 6.2 1.1 - - + -
363B ILE* 4.4 10.5 - - + -
364B LEU* 5.5 2.9 - - + -
367B PHE* 3.7 21.5 - - + -
392B VAL* 3.7 21.1 - - + -
396B CYS* 3.5 26.9 - - - -
409B LEU* 2.9 42.0 + - + +
410B LYS* 3.0 6.9 + - - +
412B ASN* 1.3 76.0 - - - +
414B ILE* 1.3 53.1 + - - +
416B ASN* 3.1 1.7 + - - +
417B VAL* 2.8 39.3 + - + +
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Residues in contact with ILE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B VAL* 4.9 1.1 - - + -
393B LYS* 3.5 49.0 - - + +
396B CYS* 3.5 25.8 - - + +
410B LYS 2.9 19.5 + - - +
411B VAL* 3.7 7.9 - - - +
413B ILE* 1.3 77.2 - - - +
415B LYS* 1.3 66.5 + - - +
417B VAL* 3.2 8.2 + - + +
418B ARG* 3.1 34.5 + - + +
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Residues in contact with LYS 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLU* 3.0 30.0 + - - +
411B VAL* 3.1 13.1 + - + +
412B ASN* 3.4 27.4 - - - +
414B ILE* 1.3 81.2 - - - +
416B ASN* 1.3 68.1 + - - +
418B ARG* 3.3 26.4 + - - +
419B ILE* 3.0 39.4 + - + +
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Residues in contact with ASN 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 3.8 11.0 - - + +
276B ASN* 3.9 10.4 - - - +
277B SER* 3.2 23.5 + - - +
280B GLU* 3.2 34.6 + - - +
412B ASN 2.9 21.7 + - - +
413B ILE 3.8 2.5 - - - +
415B LYS* 1.3 78.3 - - - +
417B VAL* 1.3 61.8 + - - +
419B ILE* 3.0 17.5 + - - +
420B ILE* 2.6 59.2 + - + +
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Residues in contact with VAL 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 3.9 22.2 - - + +
389B ILE* 4.2 24.7 - - + +
392B VAL* 3.8 28.3 - - + -
393B LYS* 4.4 14.6 - - + -
413B ILE 2.8 24.3 + - - +
414B ILE* 3.2 10.1 + - - +
416B ASN* 1.3 72.3 - - - +
418B ARG* 1.3 60.3 + - - +
421B TRP* 3.2 23.4 + - + -
422B GLU* 3.0 29.8 + - + +
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Residues in contact with ARG 418 (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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393B LYS* 3.8 25.6 - - - +
414B ILE* 3.1 22.9 + - + +
415B LYS* 3.5 32.5 + - - +
417B VAL* 1.3 76.8 - - - +
419B ILE* 1.3 80.3 + - - +
422B GLU* 3.6 16.7 - - - +
423B GLU* 3.3 28.8 + - - +
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Residues in contact with ILE 419 (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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276B ASN* 6.2 0.2 - - - +
415B LYS* 3.0 28.5 + - + +
416B ASN* 3.0 22.2 + - - +
418B ARG* 1.3 98.0 - - - +
420B ILE* 1.3 67.0 + - + +
423B GLU* 3.6 23.1 - - + +
424B ASN* 4.8 2.4 + - - -
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Residues in contact with ILE 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG* 4.6 6.5 - - - +
269B LEU* 3.7 14.4 - - + +
272B ASN* 3.8 27.6 - - + +
273B VAL* 3.5 15.3 - - + -
276B ASN* 3.7 24.9 - - + +
416B ASN* 2.6 48.2 + - + +
418B ARG 3.4 0.2 - - - -
419B ILE* 1.3 87.7 - - + +
421B TRP* 1.3 64.9 + - - +
423B GLU 4.4 0.9 - - - -
424B ASN* 2.8 30.6 + - - +
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Residues in contact with TRP 421 (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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266B SER* 3.8 22.4 - - - +
269B LEU* 3.4 24.7 - - + -
270B LEU* 4.0 29.8 - - + -
273B VAL* 4.2 10.5 - - + -
370B ILE* 4.3 10.5 - - + -
374B LEU* 4.0 20.2 - - + -
385B VAL* 4.2 5.9 - - + +
388B SER* 3.9 24.7 - - - -
389B ILE* 3.6 27.1 - - + +
392B VAL* 4.1 18.2 - - + -
416B ASN 3.7 0.2 + - - -
417B VAL* 3.2 24.6 + - + +
420B ILE* 1.3 78.3 - - - +
422B GLU* 1.3 58.1 + - - +
423B GLU 3.1 1.1 - - - -
424B ASN* 2.8 24.3 + - - +
425B LEU* 3.3 27.2 + - + +
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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
------------------------------------------------------------
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