Contacts of the helix formed by residues 398 - 410 (chain A) in PDB entry 3QFS
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A ALA 4.0 1.0 - - - +
397A SER* 1.3 77.3 - - - +
399A PRO* 1.3 77.1 - - - +
400A SER* 2.9 38.8 + - - +
401A GLU* 2.9 30.8 + - + +
402A GLN* 3.0 11.1 + - - +
439A SER* 3.0 24.8 + - - +
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Residues in contact with PRO 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A SER 3.2 11.4 - - - +
398A GLU* 1.3 93.4 - - - +
400A SER* 1.3 56.7 + - - +
402A GLN* 3.2 11.0 + - + +
403A GLU* 2.8 45.4 + - + +
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Residues in contact with SER 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A GLU* 2.9 25.4 + - - +
399A PRO* 1.3 78.2 - - - +
401A GLU* 1.3 63.0 + - - +
403A GLU* 3.4 15.6 + - - +
404A LEU* 3.0 26.2 + - - +
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Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ALA* 4.3 6.1 - - + -
398A GLU* 2.9 25.3 + - + +
400A SER* 1.3 77.6 + - - +
402A GLN* 1.3 67.0 + - - +
404A LEU* 3.2 9.0 + - + +
405A LEU* 3.0 28.2 + - - +
436A ASP 4.5 1.9 - - - +
437A CYS* 3.2 30.9 - - + +
438A PRO* 3.3 21.8 - - - +
439A SER* 2.6 42.1 + - - +
440A LEU 4.0 0.2 + - - -
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Residues in contact with GLN 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ALA* 3.1 31.0 + - + +
394A GLN* 3.7 18.0 + - - +
396A ALA* 3.5 30.4 + - - +
398A GLU 3.0 6.9 + - - +
399A PRO* 3.6 12.4 - - + +
401A GLU* 1.3 75.8 - - - +
403A GLU* 1.3 59.2 + - + +
405A LEU* 3.4 4.5 + - - +
406A ARG* 2.9 50.9 + - + +
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Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A PRO* 2.8 38.5 + - + +
400A SER* 3.5 10.9 + - - +
402A GLN* 1.3 78.4 - - + +
404A LEU* 1.3 57.0 + - - +
406A ARG* 3.4 19.7 + - - +
407A LYS* 2.9 32.0 + - - +
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A SER 3.0 14.3 + - - +
401A GLU* 3.2 11.2 + - + +
403A GLU* 1.3 76.3 - - - +
405A LEU* 1.3 61.9 + - - +
407A LYS* 3.3 8.0 + - + +
408A MET* 3.0 39.0 + - + +
418A LEU* 3.5 31.0 - - + -
422A TRP* 4.4 22.0 - - + +
436A ASP 5.9 0.2 - - - +
437A CYS* 4.1 23.1 - - - -
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A LEU* 4.3 23.0 - - + +
392A LEU* 4.7 1.8 - - + -
393A ALA* 4.0 20.6 - - + +
396A ALA* 4.1 13.2 - - + -
401A GLU 3.0 20.8 + - - +
402A GLN 3.8 3.1 - - - +
404A LEU* 1.3 76.2 - - - +
406A ARG* 1.3 62.6 + - - +
408A MET* 3.4 22.2 + - + +
409A ALA* 3.1 24.8 + - - +
433A ILE* 4.1 23.1 - - + -
437A CYS* 4.3 14.6 - - + -
440A LEU* 4.0 33.0 - - + -
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Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A TYR* 5.7 4.2 - - + +
393A ALA* 3.6 19.7 - - + -
402A GLN* 2.9 36.7 + - + +
403A GLU* 3.8 19.0 - - - +
405A LEU* 1.3 76.1 - - - +
407A LYS* 1.3 62.1 + - - +
409A ALA* 3.3 6.5 + - - +
410A SER* 3.0 24.8 + - - -
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Residues in contact with LYS 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A GLU 2.9 18.2 + - - +
404A LEU* 3.5 8.3 - - + +
405A LEU 3.2 0.2 - - - -
406A ARG* 1.3 76.7 - - - +
408A MET* 1.3 62.2 + - - +
410A SER* 2.7 25.2 + - - -
412A SER* 4.6 4.7 - - - +
414A GLU* 3.9 46.0 + - - +
415A GLY* 3.2 19.8 - - - +
418A LEU* 4.0 21.3 - - + +
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Residues in contact with MET 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A THR* 3.8 4.7 - - - +
389A LEU* 4.2 9.9 - - + -
404A LEU* 3.0 28.6 + - + +
405A LEU* 4.0 20.9 - - + +
407A LYS* 1.3 74.0 - - - +
409A ALA* 1.3 59.4 + - - +
410A SER 4.1 3.0 - - - +
415A GLY 3.7 9.7 - - - +
416A LYS* 5.4 0.2 - - - -
418A LEU* 3.4 40.2 - - + +
419A TYR* 3.4 32.5 - - + +
422A TRP* 3.4 49.6 - - + -
423A VAL* 4.0 11.0 - - + -
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Residues in contact with ALA 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A THR* 3.4 40.3 - - - +
389A LEU* 4.0 3.4 - - + -
390A TYR* 3.6 32.0 - - + +
405A LEU 3.1 17.3 + - - +
406A ARG* 3.7 5.8 - - - +
408A MET* 1.3 76.9 - - - +
410A SER* 1.3 63.4 + - - +
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Residues in contact with SER 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A THR* 5.5 1.7 - - - +
390A TYR* 6.4 0.2 - - - -
406A ARG 3.0 13.3 + - - -
407A LYS* 2.7 23.5 + - - +
408A MET 4.1 4.7 - - - +
409A ALA* 1.3 83.0 - - - +
411A SER* 1.3 58.9 + - - +
412A SER* 3.2 23.2 + - - -
416A LYS* 4.2 13.0 + - - +
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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