Contacts of the helix formed by residues 399 - 417 (chain B) in PDB entry 1EQR
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 LYS 399 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B PRO 2.8 24.9 + - - -
315B LYS* 3.1 19.3 + - + +
316B GLY 3.1 30.1 - - - +
317B ARG* 4.0 28.7 - - + +
397B ASP 3.8 1.6 + - - -
398B ASN* 1.3 75.0 + - - +
400B LYS* 1.3 55.4 + - - +
403B ALA* 3.1 28.2 + - - +
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Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ASN* 2.7 20.0 + - - +
399B LYS* 1.3 75.0 - - - +
401B ILE* 1.3 75.4 + - + +
403B ALA* 3.2 4.6 + - + +
404B ASP* 2.9 57.9 + - - +
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Residues in contact with ILE 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B TYR 3.7 17.7 - - - +
345B GLY* 3.1 39.0 - - - +
346B ALA* 3.7 6.7 - - + +
397B ASP* 3.2 37.9 - - + +
398B ASN* 2.7 22.3 + - + +
400B LYS* 1.3 79.5 - - + +
402B VAL* 1.3 57.4 + - - +
404B ASP* 4.1 0.6 - - - -
405B ALA* 2.9 33.1 + - + +
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Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 5.4 0.2 - - + -
317B ARG* 3.5 36.1 - - + +
319B ALA* 3.5 31.2 - - + -
395B GLY* 3.4 18.4 - - - +
397B ASP* 3.1 36.3 - - + +
398B ASN 3.0 6.2 + - - +
401B ILE* 1.3 74.6 - - - +
403B ALA* 1.3 61.2 + - - +
405B ALA* 4.6 3.4 - - - -
406B MET* 2.8 38.3 + - + +
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Residues in contact with ALA 403 (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 GLU* 4.5 15.3 - - + +
280B GLY* 3.3 29.5 - - - +
292B LEU* 5.5 0.4 - - - -
317B ARG* 4.7 5.2 - - - +
399B LYS 3.1 21.7 + - - +
400B LYS* 3.5 5.8 - - - +
402B VAL* 1.3 79.3 - - - +
404B ASP* 1.3 59.2 + - - +
407B GLY* 2.6 35.4 + - - +
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Residues in contact with ASP 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLY 4.8 3.8 - - - +
344B TYR* 3.7 30.6 - - + +
400B LYS* 2.9 58.1 + - - +
401B ILE 4.3 0.9 - - - +
403B ALA* 1.3 76.0 - - - +
405B ALA* 1.3 59.1 + - - +
407B GLY* 4.8 0.2 - - - -
408B ALA* 2.9 31.4 + - - +
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B PHE* 4.8 0.5 - - - -
341B VAL* 4.1 27.8 - - + +
344B TYR* 3.7 14.3 - - + +
346B ALA* 4.1 15.3 - - + +
401B ILE* 2.9 21.4 + - + +
402B VAL* 3.9 2.5 - - - +
404B ASP* 1.3 72.9 - - - +
406B MET* 1.3 61.1 + - + +
408B ALA* 3.1 4.0 + - - +
409B LEU* 2.6 36.5 + - - +
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Residues in contact with MET 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 3.8 23.6 - - + +
319B ALA* 4.2 6.1 - - + +
321B LEU* 3.5 33.2 - - + +
341B VAL* 5.0 2.0 - - - -
349B LEU* 3.8 15.9 - - - -
393B PHE* 3.9 19.3 - - + +
395B GLY* 3.7 31.4 - - - +
402B VAL* 2.8 27.8 + - + +
405B ALA* 1.3 76.0 - - + +
407B GLY* 1.3 67.5 + - - +
409B LEU* 3.7 21.9 - - + +
410B ARG* 2.8 26.5 + - - +
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Residues in contact with GLY 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B TYR 3.5 23.6 - - - +
280B GLY* 4.2 4.0 - - - -
281B SER* 5.9 1.1 - - - -
292B LEU* 4.5 1.9 - - - +
403B ALA 2.6 24.0 + - - -
406B MET* 1.3 82.9 - - - +
408B ALA* 1.3 60.3 + - - +
410B ARG* 3.3 9.8 + - - +
411B LEU* 3.4 18.0 + - - +
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Residues in contact with ALA 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B PHE* 3.7 11.5 - - + -
344B TYR* 3.5 36.8 - - + +
404B ASP 2.9 20.0 + - - +
405B ALA 3.5 2.9 - - - +
407B GLY* 1.3 76.2 - - - +
409B LEU* 1.3 61.4 + - - +
411B LEU* 3.0 20.4 + - - +
412B LYS* 3.1 11.4 + - - +
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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
----------------------------------------------------------
321B LEU* 4.3 4.9 - - + -
337B TYR* 3.8 23.8 - - + -
340B PHE* 3.7 12.9 - - + -
341B VAL* 3.5 16.2 - - + -
349B LEU* 3.6 35.9 - - + -
393B PHE* 4.2 14.4 - - + -
405B ALA 2.6 20.7 + - - +
406B MET* 3.7 21.8 - - + +
408B ALA* 1.3 69.1 - - - +
410B ARG* 1.3 66.8 + - - +
412B LYS* 5.0 0.2 - - + -
413B VAL* 3.0 43.0 + - + +
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Residues in contact with ARG 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ARG 4.8 1.1 - - - -
279B TYR* 3.4 44.2 + - - +
285B ASP 3.1 26.5 + - - +
288B ASN* 2.8 54.5 + - - +
290B MET* 3.0 40.0 + - + +
291B GLU* 4.2 4.5 - - - +
292B LEU* 4.6 3.8 - - + -
321B LEU* 3.7 20.6 - - + +
406B MET 2.8 18.8 + - - +
407B GLY 3.4 5.6 - - - +
409B LEU* 1.3 78.1 - - - +
411B LEU* 1.3 78.9 + - - +
413B VAL* 4.0 0.9 - - - +
414B GLY 3.1 19.4 + - - -
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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
----------------------------------------------------------
281B SER* 6.3 2.9 - - - -
285B ASP* 3.9 35.7 - - + +
288B ASN* 4.2 9.6 + - + +
407B GLY 3.4 10.9 + - - +
408B ALA* 3.0 13.0 + - - +
410B ARG* 1.3 95.6 - - - +
412B LYS* 1.3 62.3 + - - +
414B GLY* 3.5 1.0 + - - -
415B LYS* 3.2 40.9 + - + +
420B THR* 4.9 2.3 + - + +
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Residues in contact with LYS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLU* 5.9 6.5 - - - -
337B TYR* 4.1 14.8 - - + -
340B PHE* 3.7 50.6 - - + -
408B ALA 3.1 14.3 + - - +
409B LEU* 4.1 2.7 - - - +
411B LEU* 1.3 73.4 - - - +
413B VAL* 1.3 67.9 + - - +
415B LYS* 3.0 15.0 + - - +
416B ASP* 2.8 46.9 + - - +
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Residues in contact with VAL 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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290B MET* 4.0 8.7 - - + -
321B LEU* 4.8 4.0 - - + -
323B VAL* 3.9 21.5 - - + -
329B LEU* 6.3 0.2 - - + -
337B TYR* 3.7 28.0 - - + +
393B PHE* 4.7 9.0 - - + -
409B LEU* 3.0 43.7 + - + +
410B ARG* 4.0 2.9 - - - +
412B LYS* 1.3 75.4 - - - +
414B GLY* 1.3 66.2 + - - +
416B ASP* 3.0 2.6 + - - +
417B LEU* 2.9 49.5 + - + +
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Residues in contact with GLY 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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288B ASN* 3.7 4.5 - - - -
290B MET* 3.4 22.6 - - - +
410B ARG 3.1 8.5 + - - -
413B VAL* 1.3 79.1 - - - +
415B LYS* 1.3 59.8 + - - +
418B GLY 3.6 0.2 - - - -
419B LEU* 2.7 32.9 + - - -
420B THR* 3.2 21.7 + - - -
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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
----------------------------------------------------------
411B LEU* 3.2 33.9 + - + +
412B LYS* 3.0 14.8 + - + +
414B GLY* 1.3 74.8 - - - +
416B ASP* 1.3 68.0 + - - +
418B GLY* 3.0 14.6 + - - -
420B THR* 4.8 13.2 - - + -
422B GLU* 6.0 7.2 - - + -
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Residues in contact with ASP 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B TYR* 2.5 42.5 + - - +
412B LYS* 2.8 31.3 + - - +
413B VAL 3.0 3.7 + - - +
415B LYS* 1.3 78.4 - - - +
417B LEU* 1.3 64.5 + - + +
418B GLY 2.9 6.1 + - - -
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Residues in contact with LEU 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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323B VAL* 3.5 31.6 - - + -
324B PRO 4.8 3.4 - - - +
325B GLY 4.7 12.8 - - - +
326B GLY* 4.7 3.1 - - - -
329B LEU* 4.4 24.9 - - + -
333B GLN* 5.7 4.5 - - - +
337B TYR* 4.7 3.4 - - - +
413B VAL* 2.9 27.7 + - + +
416B ASP* 1.3 76.4 - - + +
418B GLY* 1.3 64.2 + - - +
419B LEU* 3.0 23.1 + - + +
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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