Contacts of the helix formed by residues 395 - 408 (chain B) in PDB entry 1QAS
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 LEU 395 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394B SER* 1.3 73.5 - - - +
396B GLU* 1.3 59.4 + - - +
398B GLN* 3.6 5.0 + - - +
399B ARG* 3.0 44.0 + - - +
485B LYS 3.1 22.0 - - - +
486B LEU* 3.4 15.0 - - - +
487B LYS* 3.4 33.7 - - - +
488B LEU 3.6 1.1 - - - +
489B VAL* 3.3 32.5 - - + +
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Residues in contact with GLU 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B GLN* 2.9 32.6 + - - +
394B SER* 3.1 7.6 + - - +
395B LEU* 1.3 78.5 - - - +
397B GLN* 1.3 62.4 + - - +
399B ARG* 3.1 34.4 + - - +
400B VAL* 3.3 22.1 + - - +
403B ARG* 5.8 0.9 + - - -
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Residues in contact with GLN 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ASP* 3.1 34.4 + - - +
347B GLY 2.8 44.9 + - - +
350B GLN* 3.3 44.2 + - - +
352B PRO* 3.2 17.7 - - + +
393B CYS* 4.0 10.5 - - + -
394B SER* 3.2 7.7 + - - +
396B GLU* 1.3 76.8 - - - +
398B GLN* 1.3 58.6 + - - +
400B VAL* 3.1 8.0 + - - +
401B MET* 2.9 30.5 + - - +
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Residues in contact with GLN 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ASN* 3.1 26.4 + - - +
393B CYS* 2.9 25.0 + - + +
394B SER 2.9 24.3 + - - +
395B LEU* 3.7 8.6 - - - +
396B GLU 3.2 0.2 - - - -
397B GLN* 1.3 73.8 - - - +
399B ARG* 1.3 61.1 + - - +
401B MET* 3.3 11.5 - - - +
402B ALA* 2.9 28.2 + - - +
487B LYS 3.1 21.0 + - - -
488B LEU* 3.4 11.7 - - - +
489B VAL* 3.0 39.0 + - + +
492B LEU* 3.7 9.4 - - + +
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Residues in contact with ARG 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B LEU* 3.0 41.9 + - - +
396B GLU* 3.1 38.7 + - - +
398B GLN* 1.3 75.6 - - - +
400B VAL* 1.3 58.6 + - - +
402B ALA* 3.4 7.5 + - - +
403B ARG* 2.8 58.1 + - - +
485B LYS* 5.1 3.4 + - - +
489B VAL* 3.3 23.4 - - + +
490B PRO* 5.9 0.6 - - - +
491B GLU* 3.0 28.3 + - - +
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Residues in contact with VAL 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B GLN* 3.4 26.0 - - + +
351B GLU* 3.7 5.6 - - - +
352B PRO* 3.4 23.3 - - + -
396B GLU* 3.4 23.8 - - - +
397B GLN* 3.1 11.6 + - + +
399B ARG* 1.3 77.8 - - - +
401B MET* 1.3 60.2 + - - +
403B ARG* 3.3 8.2 + - + +
404B HIS* 3.0 42.2 + - + +
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Residues in contact with MET 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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344B CYS* 3.4 29.4 - - + -
352B PRO* 3.8 18.6 - - + -
366B PHE* 3.5 28.5 - - + -
389B LEU* 4.5 11.9 - - + -
391B ASN* 3.2 31.2 - - + +
393B CYS* 3.8 13.0 - - - -
397B GLN 2.9 14.8 + - - +
398B GLN* 3.3 12.3 - - - +
400B VAL* 1.3 76.4 - - - +
402B ALA* 1.3 57.5 + - - +
404B HIS* 3.1 4.7 + - - +
405B LEU* 2.9 34.2 + - - +
492B LEU* 4.3 19.3 - - + -
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Residues in contact with ALA 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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398B GLN 2.9 17.0 + - - +
399B ARG 3.7 4.7 - - - +
401B MET* 1.3 75.1 - - - +
403B ARG* 1.3 60.7 + - + +
405B LEU* 3.3 2.6 + - - +
406B ARG* 3.1 35.8 + - - +
491B GLU* 3.7 28.5 - - + +
492B LEU* 4.1 3.3 - - + +
495B MET* 3.7 27.3 - - + +
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Residues in contact with ARG 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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396B GLU* 5.8 0.8 + - - -
399B ARG* 2.8 56.1 + - - +
400B VAL* 3.6 7.9 - - - +
401B MET 3.2 0.2 - - - -
402B ALA* 1.3 75.9 - - - +
404B HIS* 1.3 60.5 + - + +
406B ARG* 3.8 7.0 - - - +
407B ALA* 2.8 33.3 + - - +
491B GLU* 4.5 19.2 - - - +
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Residues in contact with HIS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B GLU* 2.9 34.6 + - - -
352B PRO* 4.5 1.8 - - + -
366B PHE* 4.0 21.5 - + + -
367B CYS* 3.6 29.1 - - + +
370B LEU* 3.8 5.4 - - + -
371B ARG* 5.0 4.7 + - - -
400B VAL* 3.0 35.2 + - + +
401B MET 3.5 6.3 - - - +
403B ARG* 1.3 75.3 - - + +
405B LEU* 1.3 60.0 + - - +
407B ALA* 4.4 3.4 - - - +
408B ILE* 2.7 48.6 + - + +
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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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366B PHE* 3.9 13.5 - - + -
370B LEU* 3.5 28.3 - - + -
387B LEU* 4.7 1.6 - - + -
389B LEU* 4.4 7.4 - - + -
401B MET 2.9 16.6 + - - +
402B ALA 3.5 6.7 - - - +
404B HIS* 1.3 75.5 - - - +
406B ARG* 1.3 58.4 + - - +
409B LEU* 2.9 56.8 + - + +
413B LEU* 4.5 4.9 - - + -
437B LEU* 3.6 36.6 - - + -
492B LEU* 3.9 12.3 - - + -
495B MET* 3.7 23.1 - - + -
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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
----------------------------------------------------------
402B ALA* 3.1 16.8 + - - +
403B ARG* 4.1 7.2 - - - +
405B LEU* 1.3 78.2 - - - +
407B ALA* 1.3 57.6 + - - +
410B GLY* 3.1 26.3 + - - +
413B LEU* 4.3 9.7 - - + +
415B ASP* 4.4 24.5 + - - +
491B GLU 6.0 0.4 - - - -
495B MET* 4.1 21.7 - - + +
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ARG 2.8 21.1 + - - +
404B HIS* 4.1 4.7 - - - +
406B ARG* 1.3 80.5 - - - +
408B ILE* 1.3 65.1 + - + +
410B GLY* 4.4 2.8 + - - -
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Residues in contact with ILE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B CYS* 3.2 40.4 - - + +
370B LEU* 3.6 33.7 - - + +
371B ARG* 3.8 32.5 - - + +
374B ARG* 3.3 29.9 + - - +
404B HIS* 2.7 34.4 + - + +
407B ALA* 1.3 78.8 - - + +
409B LEU* 1.3 62.7 + - + +
410B GLY* 4.6 0.3 - - - -
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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