Contacts of the helix formed by residues 398 - 408 (chain B) in PDB entry 3QFR
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 GLU 398 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396B ALA 3.6 7.1 - - - +
397B SER* 1.3 76.7 - - - +
399B PRO* 1.3 76.6 - - - +
400B SER* 2.8 48.1 + - - +
401B GLU* 3.3 23.6 + - + +
402B GLN* 3.5 7.1 + - - +
439B SER* 2.9 21.4 + - - +
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Residues in contact with PRO 399 (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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397B SER 3.3 11.0 - - - +
398B GLU* 1.3 94.7 - - - +
400B SER* 1.3 58.0 + - - +
401B GLU 3.5 0.2 - - - -
402B GLN* 3.8 24.4 + - + +
403B GLU* 3.2 16.1 + - - +
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Residues in contact with SER 400 (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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398B GLU* 2.8 29.0 + - - +
399B PRO* 1.3 69.1 - - - +
401B GLU* 1.3 70.5 + - - +
402B GLN 3.0 6.1 + - - -
403B GLU* 2.9 21.6 - - - +
404B LEU* 3.3 18.7 + - - +
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Residues in contact with GLU 401 (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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396B ALA* 4.2 4.7 - - + -
398B GLU* 3.3 17.1 + - + +
400B SER* 1.3 89.1 + - - +
402B GLN* 1.3 57.6 + - - +
404B LEU* 3.5 14.9 - - + +
405B LEU* 3.1 32.8 + - + +
436B ASP 4.9 0.7 - - - +
437B CYS* 3.3 29.8 - - + +
438B PRO* 3.5 17.8 - - - +
439B SER* 2.5 44.6 + - - +
440B LEU 3.9 0.7 + - - -
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Residues in contact with GLN 402 (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 ALA* 3.6 20.3 - - - +
394B GLN* 4.2 8.3 - - - +
396B ALA* 2.8 41.6 + - + +
397B SER 4.9 0.4 - - - +
398B GLU 3.5 4.7 + - - +
399B PRO* 3.9 18.3 - - + +
400B SER 3.0 0.8 - - - -
401B GLU* 1.3 75.7 - - - +
403B GLU* 1.3 62.3 + - - +
404B LEU 3.0 4.3 - - - -
405B LEU 3.2 9.7 + - - -
406B ARG* 3.2 48.4 + - - +
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Residues in contact with GLU 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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399B PRO 3.2 9.0 + - - +
400B SER* 2.9 35.7 + - - +
402B GLN* 1.3 76.6 - - - +
404B LEU* 1.3 67.5 + - - +
406B ARG* 3.6 16.4 - - + +
407B LYS* 3.0 31.0 + - + +
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Residues in contact with LEU 404 (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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400B SER* 3.3 17.5 + - - +
401B GLU* 3.5 17.9 - - + +
403B GLU* 1.3 80.2 - - - +
405B LEU* 1.3 65.1 + - + +
407B LYS* 2.9 31.0 - - + +
408B MET* 3.2 38.7 - - + +
418B LEU* 4.3 14.6 - - + -
422B TRP* 4.6 14.8 - - + -
437B CYS* 4.0 20.0 - - - -
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Residues in contact with LEU 405 (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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389B LEU* 3.8 28.8 - - + +
390B TYR* 3.8 17.2 + - - -
392B LEU* 4.8 0.4 - - + -
393B ALA* 3.8 28.0 - - + +
396B ALA* 4.8 3.1 - - + -
401B GLU 3.1 19.5 - - - +
402B GLN 3.2 6.8 + - - +
404B LEU* 1.3 83.9 - - + +
406B ARG* 1.3 58.8 + - - +
408B MET* 3.3 30.3 + - + +
409B ALA* 4.5 2.3 + - - +
422B TRP* 5.0 1.6 - - + -
433B ILE* 4.8 8.3 - - + -
437B CYS* 4.4 14.8 - - + -
440B LEU* 3.7 29.4 - - + -
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Residues in contact with ARG 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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390B TYR* 3.4 38.9 - - + -
393B ALA* 3.9 12.0 - - + +
394B GLN* 4.3 21.4 - - - +
402B GLN* 3.2 47.2 + - - +
403B GLU* 3.2 12.0 + - - +
405B LEU* 1.3 75.6 - - - +
407B LYS* 1.3 65.7 + - - +
408B MET 3.2 2.0 - - - -
409B ALA* 3.3 17.9 + - - +
410B SER* 3.9 2.4 + - - -
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Residues in contact with LYS 407 (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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403B GLU* 3.0 17.3 + - + +
404B LEU* 2.9 31.2 - - + +
406B ARG* 1.3 72.0 - - - +
408B MET* 1.3 57.6 + - + +
409B ALA 2.9 5.6 - - - -
410B SER* 2.8 25.5 + - - +
414B GLU* 3.3 46.1 + - - +
415B GLY* 3.1 25.1 - - - +
418B LEU* 3.6 29.4 - - + -
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Residues in contact with MET 408 (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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217B GLU* 5.3 0.3 - - - +
386B THR* 3.0 27.4 - - - +
389B LEU* 3.9 19.1 - - + -
404B LEU* 3.2 45.7 + - + +
405B LEU* 3.3 28.3 - - + +
406B ARG 3.2 0.8 - - - -
407B LYS* 1.3 77.3 - - + +
409B ALA* 1.3 56.2 + - - +
410B SER 3.4 3.1 - - - +
415B GLY 3.8 17.7 - - - +
418B LEU* 4.3 11.7 - - + +
419B TYR* 3.9 21.3 - - + +
422B TRP* 4.3 8.7 - - + -
423B VAL* 3.7 26.5 - - - -
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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