Contacts of the helix formed by residues 413 - 423 (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 GLY 413 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412B SER* 1.3 77.7 + - - +
414B GLU* 1.3 67.1 + - - -
415B GLY 3.0 4.9 + - - -
416B LYS* 3.3 10.5 + - - +
417B GLU* 3.1 25.7 + - - +
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Residues in contact with GLU 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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407B LYS* 3.3 25.4 + - - +
413B GLY* 1.3 71.8 - - - -
415B GLY* 1.3 62.7 + - - +
417B GLU* 3.5 12.9 + - - +
418B LEU* 2.9 29.5 + - + +
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Residues in contact with GLY 415 (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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407B LYS* 3.1 42.6 - - - +
408B MET* 3.8 6.3 - - - -
410B SER* 4.6 3.1 - - - -
412B SER 4.0 6.4 + - - -
413B GLY 3.0 3.4 + - - -
414B GLU* 1.3 79.6 - - - +
416B LYS* 1.3 61.5 + - - -
418B LEU* 3.3 2.8 + - - +
419B TYR* 3.0 21.0 + - - +
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Residues in contact with LYS 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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217B GLU* 3.2 40.8 + - - +
221B THR* 5.5 4.0 + - - -
410B SER 3.5 7.9 + - - +
411B SER 3.2 26.9 + - - +
412B SER* 3.4 19.7 + - - +
413B GLY 3.3 7.8 + - - +
415B GLY* 1.3 68.2 - - - +
417B GLU* 1.3 59.6 + - + +
418B LEU 2.9 1.6 - - - -
419B TYR* 2.6 30.0 + - - +
420B LEU* 2.7 34.7 + - + +
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Residues in contact with GLU 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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413B GLY* 3.1 29.8 - - - +
414B GLU* 3.5 10.8 + - - +
415B GLY 3.5 0.2 - - - -
416B LYS* 1.3 77.7 - - + +
418B LEU* 1.3 56.7 + - - +
420B LEU* 4.3 8.8 - - + +
421B SER* 2.8 32.1 + - - -
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Residues in contact with LEU 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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404B LEU* 4.3 17.7 - - + -
407B LYS* 3.6 35.9 - - + -
408B MET* 4.3 10.7 - - + +
414B GLU* 2.9 19.4 + - + +
415B GLY 3.6 3.6 - - - +
417B GLU* 1.3 78.3 - - - +
419B TYR* 1.3 58.9 + - - +
421B SER* 4.5 2.7 - - - -
422B TRP* 2.8 56.1 + - + +
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Residues in contact with TYR 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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214B ASN* 5.1 1.8 - - - -
216B GLU* 4.0 17.4 - - + +
217B GLU* 3.4 18.8 - - - +
383B PRO* 4.6 1.7 + - - +
384B PRO 2.7 23.1 + - - -
385B ARG* 3.2 12.8 + - - +
386B THR* 3.6 21.3 + - + -
389B LEU* 3.8 17.9 - - + -
408B MET* 3.9 24.4 - - + +
415B GLY 3.0 12.5 + - - +
416B LYS* 2.6 16.7 + - - +
418B LEU* 1.3 70.5 - - - +
420B LEU* 1.3 68.0 + - + +
423B VAL* 3.0 40.0 + - + +
424B VAL* 2.9 44.8 + - + +
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Residues in contact with LEU 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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214B ASN* 3.0 38.8 - - + +
217B GLU* 4.3 13.7 - - + +
416B LYS* 2.7 43.8 + - + +
417B GLU* 4.3 7.2 - - + +
419B TYR* 1.3 74.6 - - + +
421B SER* 1.3 51.5 + - - +
424B VAL* 3.5 12.0 - - + +
425B GLU* 2.6 35.3 + - - +
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Residues in contact with SER 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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417B GLU 2.8 23.0 + - - -
418B LEU* 4.3 3.4 - - - -
420B LEU* 1.3 76.6 - - - +
422B TRP* 1.3 60.4 + - - +
423B VAL 3.6 0.2 - - - -
425B GLU* 3.5 12.8 - - - +
426B ALA* 3.2 28.4 + - - +
484B LYS* 5.1 7.1 + - - +
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Residues in contact with TRP 422 (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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404B LEU* 4.6 14.1 - - + -
405B LEU* 5.0 0.4 - - + -
408B MET* 4.3 12.8 - - + -
418B LEU* 2.8 41.0 + - + +
421B SER* 1.3 76.6 - - - +
423B VAL* 1.3 75.7 + - + +
426B ALA* 3.4 8.1 - - - +
428B ARG* 2.9 70.0 + - - +
433B ILE* 4.2 24.2 - - + -
436B ASP* 3.5 33.7 - - + -
437B CYS* 3.9 28.0 - - - -
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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
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383B PRO* 3.7 20.9 - - + +
384B PRO* 3.8 17.9 - - + +
389B LEU* 4.0 8.3 - - + -
408B MET* 3.7 29.2 - - - -
419B TYR* 3.0 35.2 + - + +
422B TRP* 1.3 89.7 - - + +
424B VAL* 1.3 63.5 + - - +
427B ARG* 3.3 2.0 + - - -
428B ARG* 3.1 31.1 + - - +
433B ILE* 4.3 10.3 - - + -
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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