Contacts of the helix formed by residues 410 - 421 (chain B) in PDB entry 2QCU
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 THR 410 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403B ARG* 3.3 7.0 - - - +
408B PHE 3.5 4.7 + - - +
409B LEU* 1.3 76.2 - - - +
411B GLU* 1.3 60.3 + - - +
412B SER* 2.9 14.9 + - - -
413B LEU* 3.0 12.5 + - - +
414B ALA* 2.9 28.6 + - - +
435B VAL* 5.8 5.6 - - + +
445B GLU* 2.7 28.8 + - - +
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Residues in contact with GLU 411 (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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399B ALA* 5.6 0.2 - - - +
403B ARG* 3.3 38.6 + - - +
410B THR* 1.3 72.8 - - - +
412B SER* 1.3 56.3 + - - +
414B ALA* 3.5 2.5 + - - +
415B ARG* 3.0 30.2 + - - +
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Residues in contact with SER 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B THR* 2.9 11.6 + - - -
411B GLU* 1.3 76.9 - - - +
413B LEU* 1.3 56.9 + - - -
415B ARG* 3.3 12.4 + - - +
416B HIS* 2.9 27.0 + - - +
445B GLU* 2.7 27.3 + - - -
819B EDO 4.1 14.9 - - - -
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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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409B LEU* 3.9 10.5 - - + -
410B THR* 3.0 20.5 + - - +
412B SER* 1.3 79.6 + - - +
414B ALA* 1.3 62.0 + - - +
416B HIS* 3.1 13.1 + - + -
417B TYR* 2.9 77.2 + - + +
435B VAL* 6.2 2.0 - - + -
438B LEU* 3.8 21.1 - - + -
445B GLU* 3.6 31.4 - - + +
447B TYR* 4.0 13.2 - - + -
819B EDO 4.4 1.1 - - - -
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Residues in contact with ALA 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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399B ALA* 3.7 23.8 - - + +
402B LEU* 3.8 7.2 - - + +
403B ARG* 4.3 12.1 - - + +
409B LEU* 3.9 28.6 - - + +
410B THR 2.9 17.9 + - - +
411B GLU* 3.9 3.4 - - - +
413B LEU* 1.3 76.4 - - - +
415B ARG* 1.3 58.1 + - - +
417B TYR* 4.7 0.2 - - - -
418B ALA* 3.0 31.2 + - - +
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Residues in contact with ARG 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LYS* 5.5 4.9 - - - +
263B ASP* 3.0 38.1 + - - -
395B ARG* 3.8 13.1 - - - +
399B ALA* 4.0 13.0 - - + +
411B GLU 3.0 19.0 + - - +
412B SER* 3.5 9.6 - - - +
413B LEU 3.2 0.2 - - - -
414B ALA* 1.3 74.5 - - - +
416B HIS* 1.3 66.3 + - - +
418B ALA* 3.4 0.9 + - - +
419B ARG* 3.0 77.7 + - - +
817B EDO 6.0 1.1 - - - -
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Residues in contact with HIS 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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412B SER 2.9 13.4 + - - +
413B LEU* 3.1 12.1 + - + +
415B ARG* 1.3 78.4 - - - +
417B TYR* 1.3 70.9 + + - +
419B ARG 3.3 0.2 + - - -
420B THR* 2.7 59.3 + - + +
421B TYR* 4.3 0.8 - - - -
450B GLU* 2.8 38.4 + - - -
471B THR* 4.2 13.7 - - + -
472B LYS 5.8 0.4 - - - -
473B GLN* 3.7 18.3 + - + +
817B EDO 2.7 31.6 + - - +
819B EDO 3.7 23.1 - - - +
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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
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402B LEU* 4.0 8.3 - - + -
409B LEU* 3.9 14.8 - - + -
413B LEU* 2.9 54.4 + - + +
416B HIS* 1.3 86.0 - + - +
418B ALA* 1.3 58.4 + - - +
421B TYR* 2.8 42.9 + + + -
422B GLY 3.1 5.4 + - - -
425B SER* 3.3 18.3 + - - +
428B LEU* 3.9 22.5 - - + +
429B LEU* 3.8 32.8 - - + -
438B LEU* 4.2 11.3 - - - +
447B TYR* 4.5 7.1 - - - +
449B ALA* 5.2 0.2 - - - +
450B GLU* 3.5 29.5 + - - +
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Residues in contact with ALA 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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80B HIS* 3.6 11.1 - - - +
391B ILE* 5.3 1.7 - - - +
394B ASP* 3.8 12.1 - - - +
398B TYR* 3.8 21.4 - - + -
399B ALA* 3.7 31.4 - - + +
402B LEU* 3.9 3.0 - - + +
414B ALA 3.0 18.9 + - - +
415B ARG 3.9 2.5 - - - +
417B TYR* 1.3 76.8 - - - +
419B ARG* 1.3 60.2 + - + +
422B GLY* 3.4 21.1 + - - +
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Residues in contact with ARG 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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80B HIS 3.4 20.1 - - - +
81B ILE* 3.7 11.6 - - - +
147B ASP* 4.7 3.1 - - - +
243B LYS* 6.2 0.2 - - - +
263B ASP* 5.1 2.0 + - - -
394B ASP* 3.4 20.3 + - - +
395B ARG* 2.4 60.6 - - - +
399B ALA* 4.9 2.2 - - - +
415B ARG* 3.0 67.6 + - - +
416B HIS 4.0 2.0 - - - +
418B ALA* 1.3 76.9 - - - +
420B THR* 1.3 61.1 + - - +
808B EDO 4.0 24.7 + - - +
817B EDO 4.4 22.5 + - - +
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Residues in contact with THR 420 (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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80B HIS* 3.4 13.4 - - - -
147B ASP* 5.6 0.4 - - - +
150B ARG* 2.8 42.9 + - - +
416B HIS* 2.7 55.6 + - + +
419B ARG* 1.3 82.5 - - - +
421B TYR* 1.3 90.4 + - - +
422B GLY 3.5 0.2 - - - -
470B ARG 4.2 3.4 + - - +
471B THR* 4.6 3.2 - - + +
817B EDO 3.8 13.5 - - - +
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Residues in contact with TYR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B HIS* 4.2 2.0 - - - -
150B ARG* 3.7 6.1 - - - +
388B GLY* 3.5 9.7 - - - -
416B HIS* 4.3 1.8 - - - -
417B TYR* 2.8 27.1 + + + -
420B THR* 1.3 91.0 - - - +
422B GLY* 1.3 65.6 + - - +
423B SER 3.3 0.5 + - - -
424B ASN* 3.1 24.2 + - + +
425B SER* 3.7 22.2 - - - +
428B LEU* 3.4 27.6 - - + -
450B GLU* 2.6 35.3 + - - +
453B TYR* 3.7 14.6 - + - -
454B LEU* 3.2 31.1 - - + +
458B GLU* 3.4 27.4 - - - -
471B THR* 3.7 4.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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