Contacts of the helix formed by residues 413 - 428 (chain B) in PDB entry 1CQE
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 MET 413 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B PRO* 4.1 11.7 - - + -
397B VAL* 4.8 3.1 - - - -
402B TYR* 4.2 26.0 - - + -
406B GLN 3.7 11.0 - - - +
407B PHE* 3.7 36.1 - - + -
410B ASN* 2.7 27.8 + - + +
412B SER* 1.3 72.0 + - - +
414B LEU* 1.3 56.9 - - - +
417B TYR* 3.0 41.9 + - + +
422B LEU* 4.5 14.6 - - + -
1H NAG 3.2 36.3 - - - +
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B TYR* 3.8 16.2 + - + -
285B MET* 4.4 9.4 - - + -
296B PRO* 4.9 11.9 - - + +
299B MET* 3.8 26.0 - - + +
300B LEU* 3.8 37.2 - - + +
303B THR* 3.5 21.8 - - - +
410B ASN 5.1 1.4 + - - -
411B THR 5.5 1.7 - - - +
412B SER 3.1 1.0 + - - -
413B MET* 1.3 76.8 - - - +
415B VAL* 1.3 59.1 + - + +
418B GLY* 2.6 34.3 + - - -
419B VAL* 4.4 14.8 - - + +
422B LEU* 3.7 15.7 - - + +
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Residues in contact with VAL 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 3.8 32.1 - - + -
258B ASN* 3.3 30.7 + - - +
262B TYR* 3.9 20.9 + - + -
285B MET* 3.8 29.4 - - + -
411B THR 5.3 7.2 - - - +
412B SER* 3.4 7.2 + - - +
414B LEU* 1.3 77.9 - - + +
416B ASP* 1.3 66.1 + - - +
418B GLY* 4.0 3.5 + - - -
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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
----------------------------------------------------------
258B ASN* 5.3 1.4 + - - +
412B SER* 3.1 32.6 + - - +
413B MET 3.4 8.5 - - - +
415B VAL* 1.3 81.9 - - - +
417B TYR* 1.3 65.1 + - + +
1H NAG 2.8 29.2 + - - +
2H NAG 4.0 20.0 - - + +
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Residues in contact with TYR 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B VAL* 3.3 32.9 + - + -
400B GLN* 3.8 12.5 - - - +
402B TYR* 2.7 28.1 + + - -
413B MET* 3.0 33.9 + - + +
416B ASP* 1.3 83.1 - - + +
418B GLY* 1.3 60.5 + - - +
420B GLU* 5.5 0.2 - - - +
421B ALA* 3.0 37.4 + - + +
422B LEU* 3.9 12.8 - - + -
1H NAG 3.2 27.1 - - - -
2H NAG 5.3 5.1 + - + -
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Residues in contact with GLY 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLU* 5.6 1.8 - - - -
262B TYR* 3.6 14.8 - - - -
414B LEU* 2.6 28.1 + - - -
415B VAL 4.0 1.7 + - - -
416B ASP 3.5 1.6 - - - -
417B TYR* 1.3 79.1 - - - +
419B VAL* 1.3 67.3 + - - +
420B GLU* 3.5 6.1 - - - -
421B ALA 3.5 0.2 + - - -
422B LEU* 3.3 18.5 + - - +
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Residues in contact with VAL 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLU* 5.3 1.0 + - - -
262B TYR* 4.4 4.2 + - + -
300B LEU* 3.7 25.3 - - + +
303B THR* 3.8 29.4 - - + -
304B ILE* 3.9 19.1 - - + -
307B ARG* 3.8 17.9 - - - +
414B LEU* 4.4 5.6 - - + -
418B GLY* 1.3 71.9 - - - +
420B GLU* 1.3 67.7 + - - +
422B LEU* 3.2 1.0 + - - -
423B VAL* 2.9 34.1 + - + +
568B VAL* 4.7 1.3 - - + -
572B THR* 3.4 27.8 - - + -
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Residues in contact with GLU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLU* 3.7 15.0 - - - +
417B TYR 5.5 0.3 - - - +
418B GLY* 4.4 2.9 - - - -
419B VAL* 1.3 80.2 + - - +
421B ALA* 1.3 64.6 + - - +
423B VAL* 3.2 0.4 + - - -
424B ASP* 3.0 25.9 + - - +
572B THR* 3.5 18.1 - - - +
573B LYS* 3.1 31.8 + - - +
574B THR* 3.2 43.1 + - - +
576B PRO* 3.6 20.5 - - + +
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B VAL* 4.5 3.8 - - + +
417B TYR* 3.0 46.1 + - + +
418B GLY 3.5 0.6 + - - -
419B VAL 3.3 0.6 - - - -
420B GLU* 1.3 79.0 - - - +
422B LEU* 1.3 62.6 + - - +
424B ASP* 3.8 4.9 + - - +
425B ALA* 3.3 21.7 + - - +
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PRO* 4.9 10.5 - - + +
300B LEU* 4.1 10.5 - - + -
397B VAL* 3.9 34.3 - - + -
413B MET* 4.0 16.8 - - + +
414B LEU* 3.7 44.2 - - + +
417B TYR* 3.9 11.4 - - + -
418B GLY 3.3 11.2 + - - +
419B VAL 3.2 4.2 + - - +
421B ALA* 1.3 73.7 - - - +
423B VAL* 1.3 65.8 + - - +
425B ALA* 3.2 1.9 + - - +
426B PHE* 2.9 48.9 + - + -
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Residues in contact with VAL 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B MET* 3.6 36.1 - - + +
300B LEU* 3.8 15.0 - - + -
304B ILE* 4.2 6.5 - - + -
419B VAL* 2.9 35.3 + - + +
420B GLU 3.8 3.6 - - - +
422B LEU* 1.3 75.9 - - - +
424B ASP* 1.3 56.0 + - - +
426B PHE* 4.1 0.2 - - - -
427B SER* 2.8 38.4 + - - +
568B VAL* 4.3 5.6 - - + -
576B PRO* 3.8 19.5 - - + -
577B TYR 4.0 0.7 - - - +
578B VAL* 3.9 17.9 - - + -
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Residues in contact with ASP 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B GLU 3.0 16.1 + - - +
421B ALA* 4.0 5.6 - - - +
423B VAL* 1.3 77.5 - - - +
425B ALA* 1.3 63.2 + - - +
427B SER* 3.4 1.7 + - - -
428B ARG* 2.7 65.6 + - - +
576B PRO* 3.6 11.1 - - + +
577B TYR* 3.2 29.5 + - - -
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Residues in contact with ALA 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ARG 3.9 21.0 - - - +
397B VAL* 4.0 22.9 - - + -
398B GLY 4.8 3.1 - - - +
421B ALA 3.3 16.6 + - - +
422B LEU* 3.2 6.3 + - - +
424B ASP* 1.3 78.1 + - - +
426B PHE* 1.3 68.7 + - + +
428B ARG* 3.0 16.3 + - - +
429B GLN* 3.1 15.2 + - - +
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Residues in contact with PHE 426 (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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195B ASN* 3.4 2.1 - - - +
196B LEU* 3.0 43.1 + - + -
197B MET* 3.6 22.0 - - + +
200B PHE* 3.6 31.2 - + + -
296B PRO* 4.7 3.1 - - + -
297B GLY* 3.8 16.8 - - - -
300B LEU* 3.8 22.9 - - + -
395B PHE* 5.3 2.9 - + + -
396B ARG 5.4 2.2 - - - -
397B VAL* 4.6 9.4 - - + -
407B PHE* 3.7 33.4 - + - -
422B LEU* 2.9 41.6 + - + +
423B VAL 4.3 1.8 - - - +
425B ALA* 1.3 81.1 - - + +
427B SER* 1.3 60.4 + - - +
428B ARG 3.3 0.7 + - - -
429B GLN* 3.5 4.6 - - - +
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Residues in contact with SER 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ASN* 2.6 25.9 + - - +
197B MET* 3.5 10.2 - - - +
423B VAL* 2.8 23.9 + - - +
424B ASP 3.7 2.0 - - - -
425B ALA 3.1 0.2 - - - -
426B PHE* 1.3 75.6 - - - +
428B ARG* 1.3 56.8 - - - +
577B TYR* 3.1 47.1 + - - -
578B VAL* 3.6 1.7 - - - -
579B SER 3.3 20.0 + - - -
582B VAL* 3.6 0.7 - - - -
583B PRO* 3.3 4.7 - - - +
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Residues in contact with ARG 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ASP* 2.7 47.1 + - - +
425B ALA* 3.0 6.3 + - - +
427B SER* 1.3 81.3 - - - +
429B GLN* 1.3 58.6 + - - +
430B PRO* 3.5 4.2 - - - +
577B TYR* 3.6 20.6 - - + +
582B VAL* 2.8 19.5 - - - +
583B PRO* 3.7 30.9 - - + +
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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