Contacts of the helix formed by residues 400 - 414 (chain A) in PDB entry 3D0G
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 PHE 400 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A TYR* 3.8 16.2 - - + +
396A ALA* 3.5 32.8 - - + +
397A ASN* 2.9 52.2 + - - +
398A GLU 3.3 0.2 - - - -
399A GLY* 1.3 79.7 - - - +
401A HIS* 1.3 68.4 + - - +
403A ALA* 2.9 15.0 + - - +
404A VAL* 3.1 13.9 + - - +
521A TYR* 3.8 20.2 - + - -
525A PHE* 3.9 21.9 - + - -
557A MET* 3.9 22.7 - - + -
566A TRP* 3.8 23.8 - + + -
569A ALA* 4.1 8.5 - - + -
570A LEU* 4.4 11.7 - - + -
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Residues in contact with HIS 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A HIS* 2.6 47.0 + + + -
381A TYR* 3.6 27.6 - + - -
382A ASP* 2.8 34.5 + - - -
385A TYR* 3.1 11.7 + - - -
394A ASN* 4.0 8.3 - - - -
395A GLY* 3.5 26.2 - - - -
397A ASN 4.2 3.2 + - - -
398A GLU 4.7 3.4 + - - +
400A PHE* 1.3 77.4 - - - +
402A GLU* 1.3 65.0 + - + +
404A VAL* 3.1 6.6 + - - +
405A GLY 3.0 15.6 + - - -
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Residues in contact with GLU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A HIS* 3.1 22.2 + - - -
375A GLU* 5.1 0.7 - - - +
378A HIS* 2.8 33.0 + - + -
398A GLU 5.4 5.9 + - - +
399A GLY 5.0 0.6 + - - +
400A PHE 3.4 0.4 - - - -
401A HIS* 1.3 78.7 - - + +
403A ALA* 1.3 52.8 + - - +
405A GLY* 2.9 1.0 + - - -
406A GLU* 2.7 38.5 + - - +
515A TYR* 5.7 6.9 - - + -
518A ARG* 3.5 35.9 + - + +
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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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399A GLY 3.3 16.4 - - - +
400A PHE* 2.9 12.0 + - - +
402A GLU* 1.3 77.3 - - - +
404A VAL* 1.3 62.9 + - - +
406A GLU 3.4 0.2 + - - -
407A ILE* 3.2 28.5 + - - +
518A ARG* 3.7 15.9 - - + +
521A TYR* 4.1 11.2 - - + -
522A GLN* 3.9 15.3 - - + +
525A PHE* 3.9 19.1 - - + -
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Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLY 4.1 22.4 - - - +
378A HIS 5.0 0.2 - - - +
380A GLN* 6.3 0.2 - - + -
381A TYR* 4.0 13.7 - - + -
400A PHE 3.1 10.6 + - - +
401A HIS 3.1 8.7 + - - +
403A ALA* 1.3 71.2 - - - +
405A GLY* 1.3 67.1 + - - +
407A ILE* 3.5 11.0 - - - +
408A MET* 3.3 35.2 - - + +
525A PHE* 4.3 5.6 - - + -
554A LEU* 4.9 4.3 - - + -
557A MET* 3.8 29.2 - - + -
558A LEU* 3.8 22.2 - - + -
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Residues in contact with GLY 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A HIS* 3.5 48.9 - - - +
377A GLY* 5.0 0.9 - - - -
378A HIS* 4.6 2.4 - - - -
401A HIS 3.0 9.1 + - - -
402A GLU 2.9 7.0 + - - -
404A VAL* 1.3 79.1 - - - +
406A GLU* 1.3 61.8 + - - +
408A MET* 3.2 11.9 + - - +
409A SER 3.4 7.8 + - - -
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Residues in contact with GLU 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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374A HIS* 2.7 29.9 + - + -
402A GLU 2.7 20.7 + - - +
403A ALA 4.0 1.3 - - - +
405A GLY* 1.3 68.5 - - - +
407A ILE* 1.3 66.5 + - - +
409A SER* 2.9 19.6 + - - -
410A LEU* 2.9 31.1 + - + +
446A ILE* 6.0 2.1 - - - +
518A ARG* 3.7 29.2 + - - +
522A GLN* 3.9 29.0 + - - +
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Residues in contact with ILE 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 3.2 19.6 + - - +
404A VAL* 3.5 10.3 - - - +
406A GLU* 1.3 73.3 - - - +
408A MET* 1.3 83.5 + - + +
410A LEU* 3.0 18.6 + - + +
411A SER* 3.2 13.9 + - - -
522A GLN* 3.0 33.2 - - + +
525A PHE* 3.9 18.8 - - + -
526A GLN* 3.6 38.2 + - + +
529A LEU* 4.5 7.6 - - + -
544A ILE* 4.4 13.0 - - + -
554A LEU* 5.4 3.1 - - + -
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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
----------------------------------------------------------
314A PHE* 3.8 20.5 - - + -
315A PHE* 3.5 36.8 - - + -
373A HIS* 3.2 29.1 - - + +
377A GLY* 4.0 5.2 - - - -
404A VAL* 3.3 34.5 - - + +
405A GLY 3.6 3.4 - - - +
406A GLU 3.2 0.8 - - - -
407A ILE* 1.3 94.6 - - + +
409A SER* 1.3 62.7 + - - +
411A SER* 3.5 1.6 + - - -
412A ALA* 3.2 25.6 + - - +
544A ILE* 4.8 3.4 - - + -
554A LEU* 3.8 26.2 - - + -
558A LEU* 6.0 0.2 - - + -
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Residues in contact with SER 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU* 3.8 31.5 - - - +
373A HIS* 4.4 2.6 - - - +
374A HIS* 4.6 5.6 - - - +
405A GLY 3.4 5.2 + - - -
406A GLU* 2.9 28.0 + - - -
408A MET* 1.3 79.6 - - - +
410A LEU* 1.3 65.9 + - - +
412A ALA* 3.6 1.5 + - - -
413A ALA* 3.3 25.6 + - - +
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Residues in contact with LEU 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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406A GLU* 2.9 17.8 + - + +
407A ILE* 3.0 15.7 + - + +
409A SER* 1.3 84.5 + - - +
411A SER* 1.3 61.9 + - - +
413A ALA* 3.6 7.1 + - + +
414A THR* 3.3 19.8 + - - +
438A PHE* 5.9 0.9 - - + -
442A GLN* 3.7 22.4 - - - +
446A ILE* 5.4 4.0 - - + -
522A GLN* 4.6 13.5 - - + +
523A PHE* 4.2 22.0 - - + -
526A GLN* 3.8 31.6 - - + +
542A CYS 4.9 0.7 - - - -
587A TYR* 3.8 18.4 - - + +
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Residues in contact with SER 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 4.2 12.1 - - - -
407A ILE 3.2 12.5 + - - -
408A MET 3.5 0.4 + - - -
409A SER 3.5 0.2 - - - -
410A LEU* 1.3 77.2 - - - +
412A ALA* 1.3 58.6 + - - +
414A THR* 2.8 23.9 + - - -
417A HIS* 3.3 7.7 - - - +
526A GLN* 4.0 14.8 + - - -
542A CYS 3.9 8.5 - - - -
543A ASP* 3.6 21.9 - - - -
544A ILE* 3.6 30.5 + - - +
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Residues in contact with ALA 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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314A PHE* 5.2 1.7 - - + -
369A PHE* 4.2 3.2 - - + -
370A LEU* 3.7 18.6 - - + -
373A HIS* 3.8 32.1 - - + +
408A MET 3.2 17.8 + - - +
409A SER 4.0 0.4 - - - +
410A LEU 3.3 0.2 - - - -
411A SER* 1.3 79.3 - - - +
413A ALA* 1.3 59.1 + - - +
417A HIS* 3.3 31.0 - - + +
418A LEU* 3.6 13.7 - - - +
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Residues in contact with ALA 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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291A ILE* 5.0 6.8 - - + +
366A MET* 4.7 6.4 - - + +
370A LEU* 3.7 24.9 - - + -
409A SER* 3.3 16.3 + - - +
410A LEU* 3.6 3.8 + - - +
411A SER 3.3 0.4 - - - -
412A ALA* 1.3 75.7 - - - +
414A THR* 1.3 68.5 + - - +
415A PRO* 3.4 4.5 - - - +
418A LEU* 3.1 16.9 - - - +
438A PHE* 5.5 15.5 - - + -
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Residues in contact with THR 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 LEU 3.3 15.9 - - - +
411A SER 2.8 16.5 + - - +
413A ALA* 1.3 79.7 - - - +
415A PRO* 1.4 63.8 - - - +
416A LYS* 4.1 3.3 - - - +
417A HIS* 2.8 32.9 + - - +
418A LEU* 3.1 10.4 + - - +
438A PHE* 6.3 2.5 - - + -
540A HIS 3.9 11.4 - - - +
541A LYS* 3.5 22.2 - - - +
542A CYS 2.8 26.8 + - - +
543A ASP* 3.6 6.8 + - - +
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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