Contacts of the helix formed by residues 404 - 420 (chain A) in PDB entry 1W7L
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 ASP 404 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ASP* 2.8 26.1 + - - +
40A PHE* 3.5 21.6 - - + +
403A LYS* 1.3 75.9 - - - +
405A GLU* 1.3 69.9 + - - +
406A ALA* 3.0 32.0 + - + +
407A THR* 3.0 23.0 + - - +
408A LEU* 3.2 11.2 + - - +
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Residues in contact with GLU 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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315A ARG* 5.9 0.5 + - - -
319A HIS* 5.5 1.2 - - + +
403A LYS 3.7 1.6 + - - -
404A ASP* 1.3 76.4 + - - +
406A ALA* 1.3 57.4 + - - +
408A LEU* 3.2 13.7 + - + +
409A GLN* 2.9 42.6 + - + +
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Residues in contact with ALA 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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404A ASP* 3.0 15.9 + - - +
405A GLU* 1.3 77.9 - - - +
407A THR* 1.3 56.6 + - - +
409A GLN* 3.4 17.5 + - - +
410A ALA* 3.0 28.1 + - - +
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Residues in contact with THR 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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31A VAL* 3.7 20.3 - - + +
32A ASN 5.2 3.6 - - - +
33A LEU* 4.4 4.3 - - + -
39A ASP* 2.5 30.7 + - - +
403A LYS* 3.9 21.8 - - + -
404A ASP* 3.0 15.4 + - - +
406A ALA* 1.3 77.4 - - - +
408A LEU* 1.3 58.3 + - - +
410A ALA* 3.2 7.4 + - - +
411A MET* 2.9 27.0 + - - +
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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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33A LEU* 4.7 2.2 - - + -
316A CYS* 3.9 42.6 - - + +
319A HIS* 3.8 29.8 - - + +
320A MET* 3.8 29.6 - - + -
401A PHE 4.5 2.2 - - - +
403A LYS* 4.0 22.0 - - + +
404A ASP 3.7 9.0 - - - +
405A GLU* 3.2 12.4 + - + +
407A THR* 1.3 75.5 - - - +
409A GLN* 1.3 59.9 + - - +
411A MET* 3.3 15.0 + - + +
412A ASP* 3.0 34.2 + - - -
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Residues in contact with GLN 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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319A HIS* 5.6 5.4 - - + -
405A GLU* 2.9 28.8 + - + +
406A ALA* 3.5 19.7 - - - +
407A THR 3.3 0.2 - - - -
408A LEU* 1.3 76.3 - - - +
410A ALA* 1.3 62.0 + - - +
412A ASP* 3.2 11.5 + - - +
413A GLU* 3.0 24.0 + - - +
416A ARG* 4.6 2.4 + - - +
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Residues in contact with ALA 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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31A VAL* 3.8 16.8 - - + -
406A ALA 3.0 14.5 + - - +
407A THR* 3.2 10.3 + - + +
409A GLN* 1.3 72.7 - - - +
411A MET* 1.3 64.8 + - - +
413A GLU* 3.3 10.3 + - - +
414A LYS* 3.1 25.3 + - - +
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Residues in contact with MET 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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31A VAL* 3.9 16.5 - - + +
33A LEU* 3.7 17.7 - - + -
319A HIS* 4.2 4.3 - - + +
320A MET* 3.7 41.7 - - - -
323A SER* 3.8 15.5 - - - +
324A LEU* 4.5 4.7 - - + -
376A LEU* 4.2 9.2 - - + -
407A THR 2.9 13.6 + - - +
408A LEU* 3.4 29.2 - - + +
409A GLN 3.3 0.2 - - - -
410A ALA* 1.3 76.1 - - - +
412A ASP* 1.3 77.2 + - - +
414A LYS* 3.1 5.4 + - - +
415A LEU* 2.9 41.4 + - + +
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Residues in contact with ASP 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A HIS* 2.6 28.3 + - - -
323A SER* 2.6 31.9 + - - -
408A LEU 3.0 13.0 + - - +
409A GLN* 3.2 11.9 + - - +
411A MET* 1.3 79.9 - - - +
413A GLU* 1.3 57.5 + - - +
415A LEU* 3.2 6.3 + - - +
416A ARG* 2.8 58.9 + - - +
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Residues in contact with GLU 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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409A GLN 3.0 14.0 + - - +
410A ALA* 3.6 12.1 - - - +
411A MET 3.2 0.2 - - - -
412A ASP* 1.3 77.2 - - - +
414A LYS* 1.3 62.7 + - + +
416A ARG* 2.8 38.8 + - - +
417A LYS* 3.1 24.9 + - - +
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Residues in contact with LYS 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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29A ASP* 2.9 34.2 + - - +
30A VAL 4.5 0.2 - - - -
31A VAL* 3.7 21.3 - - + +
374A LYS 3.5 25.6 - - - +
375A GLY* 3.5 23.9 - - - +
376A LEU* 3.8 12.8 - - + -
410A ALA 3.1 16.4 + - - +
411A MET 3.1 6.5 + - - +
413A GLU* 1.3 75.7 - - + +
415A LEU* 1.3 57.9 - - - +
417A LYS* 3.5 11.0 + - + +
418A TRP* 3.0 26.9 + - - +
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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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323A SER* 3.7 39.0 - - - +
324A LEU* 4.1 16.8 - - + -
327A VAL* 3.7 29.9 - - + +
329A LEU* 5.2 1.3 - - + -
376A LEU* 3.8 23.6 - - + -
411A MET* 2.9 32.3 + - + +
412A ASP* 3.7 7.4 - - - +
414A LYS* 1.3 74.7 - - - +
416A ARG* 1.3 59.0 + - + +
418A TRP* 3.4 16.7 + - + +
419A LYS* 2.9 28.9 + - - +
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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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409A GLN* 4.6 2.6 + - - +
412A ASP* 2.8 47.1 + - - +
413A GLU* 2.8 39.6 + - - +
415A LEU* 1.3 70.3 - - + +
417A LYS* 1.3 64.7 + - - +
419A LYS* 3.2 17.3 + - - +
420A VAL* 3.4 17.3 + - - +
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Residues in contact with LYS 417 (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 ASN 5.8 1.4 + - - -
413A GLU* 3.1 15.1 + - - +
414A LYS* 3.6 15.5 - - + +
416A ARG* 1.3 74.8 - - - +
418A TRP* 1.3 62.3 + - - +
420A VAL* 3.3 26.9 + - + +
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Residues in contact with TRP 418 (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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327A VAL* 3.7 20.2 - - + +
329A LEU* 4.7 11.4 - - + -
347A PHE* 3.7 31.9 - + - -
366A PHE* 4.3 9.0 - + - -
369A TRP* 3.8 16.3 - + - -
370A MET* 3.8 37.0 - - + -
374A LYS* 3.5 46.4 + - + +
376A LEU* 3.8 14.6 - - + -
414A LYS 3.0 13.4 + - - +
415A LEU* 3.4 29.8 - - + +
417A LYS* 1.3 77.2 - - - +
419A LYS* 1.3 62.5 + - - +
420A VAL 3.2 4.9 + - - +
421A GLU 3.3 17.2 - - - +
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Residues in contact with LYS 419 (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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326A SER* 3.8 20.4 + - - +
327A VAL* 3.9 26.0 - - + -
415A LEU 2.9 11.3 + - - +
416A ARG* 3.2 14.1 + - - +
418A TRP* 1.3 75.7 - - - +
420A VAL* 1.3 51.4 + - + +
421A GLU 2.8 22.3 + - - +
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Residues in contact with VAL 420 (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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416A ARG 3.5 15.3 - - - +
417A LYS* 3.5 14.7 - - + +
418A TRP 3.4 4.3 - - - +
419A LYS* 1.3 71.8 - - + +
421A GLU* 1.3 68.6 + - + +
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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