Contacts of the helix formed by residues 400 - 416 (chain A) in PDB entry 1XB7
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 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A ARG* 3.5 29.2 - - - +
398A LEU 3.3 0.8 + - - -
399A GLY* 1.3 69.0 - - - -
401A LEU* 1.3 63.6 + - - +
402A GLY 3.3 2.2 - - - -
403A ALA* 3.3 18.2 + - + +
404A ALA* 3.3 11.6 + - - +
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Residues in contact with LEU 401 (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 LEU* 3.1 33.2 + - + +
399A GLY 3.2 0.6 - - - -
400A GLU* 1.3 78.9 - - - +
402A GLY* 1.3 57.1 + - - +
404A ALA* 3.1 6.5 + - + +
405A LEU* 2.9 41.2 + - + +
490A LYS* 3.6 39.7 - - + +
491A VAL* 3.8 24.9 - - + +
494A HIS* 3.9 32.3 - - + -
495A PHE* 4.2 12.1 - - + -
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Residues in contact with GLY 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 3.7 21.7 - - - +
390A GLU* 4.6 8.3 - - - -
393A ALA* 4.5 17.2 - - - +
398A LEU* 5.0 1.0 - - - +
399A GLY 4.3 4.8 + - - -
400A GLU 3.3 0.6 - - - -
401A LEU* 1.3 79.3 - - - +
403A ALA* 1.3 55.5 + - - +
405A LEU* 3.4 1.2 + - - -
406A LEU* 2.9 40.2 + - - +
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Residues in contact with ALA 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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390A GLU* 4.1 29.4 - - + +
394A ARG* 5.7 2.7 - - - +
400A GLU* 3.3 15.9 + - + +
401A LEU 3.2 0.4 - - - -
402A GLY* 1.3 72.7 - - - +
404A ALA* 1.3 65.7 + - - +
406A LEU* 3.4 4.6 + - - +
407A GLN* 3.1 22.7 + - - +
410A ARG* 4.8 2.9 + - - -
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Residues in contact with ALA 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 GLU 3.3 8.3 + - - +
401A LEU* 3.1 14.2 + - + +
403A ALA* 1.3 78.1 - - - +
405A LEU* 1.3 64.0 + - + +
407A GLN* 3.3 26.3 + - - +
408A LEU 3.4 4.7 + - - -
483A LEU* 5.5 0.3 - - - +
487A THR* 4.0 20.2 + - + +
490A LYS* 4.1 33.9 - - + +
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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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366A VAL* 3.8 39.0 - - + +
369A VAL* 4.9 12.3 - - + -
370A ALA* 5.9 1.1 - - + +
380A LEU* 3.6 23.1 - - + -
382A PHE* 3.9 31.4 - - + -
401A LEU* 2.9 32.7 + - + +
402A GLY 4.6 0.2 - - - +
404A ALA* 1.3 79.0 - - + +
406A LEU* 1.3 55.7 + - - +
408A LEU* 3.3 7.6 + - + +
409A VAL* 3.1 31.2 + - + +
487A THR* 3.9 11.9 - - + -
491A VAL* 4.5 10.8 - - + -
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ASP* 3.8 26.7 - - + +
379A GLU* 3.7 27.4 - - - +
380A LEU* 3.8 23.1 - - + -
390A GLU* 4.1 28.7 - - + +
402A GLY 2.9 23.2 + - - +
403A ALA* 3.4 4.5 + - - +
404A ALA 3.3 0.2 - - - -
405A LEU* 1.3 73.9 - - - +
407A GLN* 1.3 61.5 + - - +
409A VAL* 3.6 11.5 - - + +
410A ARG* 2.9 52.8 + - + +
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Residues in contact with GLN 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 ALA 3.1 12.8 + - - +
404A ALA* 3.3 17.1 - - - +
406A LEU* 1.3 78.0 - - - +
408A LEU* 1.3 60.9 + - - +
410A ARG* 3.5 21.0 + - - +
411A ARG* 3.2 21.7 + - - +
483A LEU* 3.7 25.6 - - + +
490A LYS* 4.9 9.5 + - - -
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Residues in contact with LEU 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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366A VAL* 3.7 29.6 - - + -
367A LEU* 5.1 0.4 - - + -
370A ALA* 3.9 21.3 - - + -
404A ALA 3.4 3.1 + - - +
405A LEU* 3.3 11.3 + - + +
407A GLN* 1.3 74.7 - - - +
409A VAL* 1.3 67.1 + - - +
411A ARG* 3.2 4.6 + - + +
412A LEU* 3.0 38.5 + - + +
480A THR* 4.4 8.1 - - - +
483A LEU* 3.7 15.6 - - + +
484A LEU* 3.9 35.2 - - + +
487A THR* 4.1 20.0 - - + +
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Residues in contact with VAL 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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369A VAL* 6.0 0.2 - - + -
370A ALA* 3.9 28.3 - - + -
373A SER* 3.9 22.0 - - - +
374A LEU* 3.9 7.2 - - + +
376A LEU 5.6 0.2 - - - +
379A GLU 5.3 0.9 - - - +
380A LEU* 4.0 18.6 - - + -
405A LEU* 3.1 15.8 + - + +
406A LEU* 3.3 17.2 + - + +
408A LEU* 1.3 76.9 - - - +
410A ARG* 1.3 59.6 + - + +
412A LEU* 3.2 4.4 + - - +
413A GLN* 2.9 50.0 + - + +
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Residues in contact with ARG 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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378A ASP* 5.0 10.0 + - - -
403A ALA 4.8 2.6 + - - -
406A LEU* 2.9 45.7 + - + +
407A GLN* 3.7 27.5 - - - +
408A LEU 3.3 0.2 - - - -
409A VAL* 1.3 70.5 - - + +
411A ARG* 1.3 65.6 + - - +
413A GLN* 3.5 16.8 - - - +
414A ALA* 3.0 25.3 + - - +
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Residues in contact with ARG 411 (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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407A GLN 3.2 12.0 + - - +
408A LEU* 3.2 10.6 + - + +
410A ARG* 1.3 80.2 - - - +
412A LEU* 1.3 59.8 + - - +
414A ALA* 3.7 15.9 - - - +
415A LEU* 3.8 12.2 + - - +
476A ARG 5.0 1.0 + - - -
479A LEU* 3.2 44.3 + - - +
480A THR* 3.9 23.5 - - + +
483A LEU* 3.9 25.0 - - + +
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Residues in contact with LEU 412 (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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367A LEU* 4.0 15.3 - - + -
370A ALA* 3.7 30.3 - - + -
371A GLN 5.3 0.9 - - - +
374A LEU* 3.7 22.0 - - + +
408A LEU* 3.0 30.2 + - + +
409A VAL 3.8 1.3 - - - +
411A ARG* 1.3 74.6 - - - +
413A GLN* 1.3 66.7 + - - +
415A LEU* 3.1 18.4 + - + +
416A ARG 3.3 8.8 + - - -
417A LEU* 3.8 31.5 + - + +
425A LEU* 4.7 9.2 - - + -
480A THR* 3.8 31.2 - - + +
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Residues in contact with GLN 413 (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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373A SER 3.8 4.9 + - - -
374A LEU* 2.5 43.3 + - + +
376A LEU 3.0 20.8 + - - -
377A GLN* 5.1 1.2 - - - +
409A VAL* 2.9 24.2 + - - +
410A ARG* 3.2 25.4 + - - +
412A LEU* 1.3 74.7 - - - +
414A ALA* 1.3 64.5 - - - +
416A ARG* 3.0 24.7 + - - +
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Residues in contact with ALA 414 (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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410A ARG 3.0 15.8 + - - +
411A ARG* 3.7 11.4 - - - +
413A GLN* 1.3 75.5 - - - +
415A LEU* 1.3 63.4 + - + +
416A ARG* 3.7 5.2 + - - +
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Residues in contact with LEU 415 (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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411A ARG* 4.0 10.3 - - - +
412A LEU* 3.1 13.5 + - + +
413A GLN 3.1 1.0 - - - -
414A ALA* 1.3 80.6 - - + +
416A ARG* 1.3 65.3 + - - +
417A LEU* 4.2 8.3 - - + +
473A ARG* 2.9 40.0 + - - +
476A ARG* 3.6 43.7 - - + +
477A LEU* 3.5 29.4 - - + -
480A THR* 3.9 15.7 - - + -
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Residues in contact with ARG 416 (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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412A LEU 3.3 1.9 + - - -
413A GLN* 3.0 21.1 + - - +
414A ALA 4.3 4.9 - - - +
415A LEU* 1.3 81.2 - - - +
417A LEU* 1.3 66.5 + - - +
418A GLU* 3.3 9.2 + - - +
473A ARG* 3.4 6.6 + - - +
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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