Contacts of the helix formed by residues 389 - 405 (chain P) in PDB entry 3HX0
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 ARG 389 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387P MET 4.5 0.7 - - - -
388P PRO* 1.3 70.5 - - - +
390P GLU* 1.3 58.4 + - - +
392P ALA* 3.6 4.6 + - - +
393P THR* 2.8 29.3 + - - +
418P TYR* 3.0 65.7 + - + +
419P ARG* 5.9 0.2 - - - +
421P GLY* 3.9 16.4 - - - -
422P LYS 3.7 15.0 + - - +
423P ALA* 2.7 25.7 + - - +
425P CYS* 4.6 9.4 - - - -
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Residues in contact with GLU 390 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388P PRO* 2.7 12.8 + - + +
389P ARG* 1.3 73.1 - - - +
391P GLU* 1.3 65.4 + - - +
393P THR* 3.0 18.8 + - - -
394P GLU* 3.1 21.1 + - + +
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Residues in contact with GLU 391 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387P MET* 3.0 31.3 - - + +
388P PRO* 2.8 23.3 + - + +
390P GLU* 1.3 75.3 - - - +
392P ALA* 1.3 62.1 + - - +
394P GLU* 3.2 17.3 + - - +
395P ILE* 3.0 30.3 + - + +
479P LEU* 4.2 9.2 + - + +
484P ARG* 3.5 26.7 + - - +
485P ARG* 4.1 21.5 + - - +
487P ARG* 3.1 23.4 + - - -
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Residues in contact with ALA 392 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387P MET* 3.6 18.9 - - + -
388P PRO 3.4 5.5 + - - +
389P ARG* 3.7 11.9 - - - +
390P GLU 3.2 0.4 - - - -
391P GLU* 1.3 75.0 - - - +
393P THR* 1.3 66.3 + - - +
395P ILE* 3.2 4.8 + - - +
396P GLU* 2.9 22.7 + - - +
418P TYR* 4.0 18.8 - - + -
425P CYS* 4.6 7.9 - - + -
428P VAL* 3.6 24.8 - - + +
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Residues in contact with THR 393 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389P ARG* 2.8 21.5 + - - +
390P GLU* 3.0 10.7 + - - -
392P ALA* 1.3 77.0 - - - +
394P GLU* 1.3 66.0 + - - +
396P GLU* 3.1 23.1 - - + +
397P GLN* 3.4 12.3 + - + +
418P TYR* 2.9 31.6 + - - +
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Residues in contact with GLU 394 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390P GLU* 3.1 14.3 + - - +
391P GLU* 3.3 18.7 + - - +
393P THR* 1.3 78.1 - - + +
395P ILE* 1.3 64.5 + - - +
396P GLU 3.0 1.2 + - - -
397P GLN* 3.1 16.2 + - - +
398P THR* 3.2 14.2 + - - -
479P LEU* 3.3 22.0 - - + +
484P ARG* 3.0 32.2 + - - -
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Residues in contact with ILE 395 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387P MET* 3.7 34.5 - - + -
391P GLU* 3.0 13.7 + - + +
392P ALA 3.4 5.6 - - - +
394P GLU* 1.3 76.5 - - - +
396P GLU* 1.3 64.9 + - - +
398P THR* 3.1 22.4 + - - -
399P VAL* 3.4 7.4 + - - +
428P VAL* 3.8 10.8 - - + -
456P PHE* 3.8 18.4 - - + -
477P CYS* 4.0 9.0 - - - -
478P ARG* 6.1 0.7 - - - -
479P LEU* 3.9 19.7 - - + +
487P ARG* 4.0 16.2 - - + -
488P ARG 5.7 0.2 - - - +
489P LEU* 3.8 26.9 - - + -
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Residues in contact with GLU 396 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392P ALA 2.9 12.7 + - - +
393P THR* 3.1 16.8 - - + +
394P GLU 3.0 0.4 + - - -
395P ILE* 1.3 79.1 - - - +
397P GLN* 1.3 83.9 + - - +
399P VAL* 3.3 4.3 + - - +
400P GLN* 2.6 59.1 + - - +
412P CYS* 4.0 18.5 - - - +
413P VAL* 5.0 0.6 - - - -
414P ALA* 4.0 28.9 + - + +
418P TYR* 5.5 3.4 - - + +
428P VAL* 4.7 2.2 - - + +
430P VAL* 4.5 18.5 - - + +
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Residues in contact with GLN 397 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393P THR* 3.4 11.6 + - + +
394P GLU* 3.1 8.4 + - - +
396P GLU* 1.3 95.0 + - - +
398P THR* 1.3 58.1 + - - +
400P GLN* 3.3 20.0 + - + +
401P LYS* 2.6 37.7 + - + +
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Residues in contact with THR 398 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394P GLU 3.2 7.4 + - - -
395P ILE* 3.1 12.1 + - - -
397P GLN* 1.3 79.3 - - - +
399P VAL* 1.3 62.1 + - - +
401P LYS* 4.0 3.1 - - - +
402P ALA* 3.5 20.1 + - - +
451P LEU* 4.1 5.4 - - + +
454P GLU* 5.4 4.6 - - - +
456P PHE* 3.8 39.3 - - + -
479P LEU* 3.2 24.5 - - + +
480P PRO* 6.0 2.0 - - + -
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Residues in contact with VAL 399 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395P ILE 3.8 11.2 - - - +
396P GLU 3.3 5.5 + - - +
398P THR* 1.3 74.2 - - - +
400P GLN* 1.3 61.7 + - - +
402P ALA* 3.4 1.7 + - - +
403P ALA* 2.8 32.8 + - - +
430P VAL* 4.6 12.3 - - + -
432P ILE* 4.3 10.3 - - + -
447P LEU* 3.7 25.3 - - + +
451P LEU* 3.9 23.6 - - + -
456P PHE* 4.2 7.0 - - + -
489P LEU* 3.9 31.0 - - + -
491P ILE* 3.9 12.1 - - + -
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Residues in contact with GLN 400 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396P GLU* 2.6 55.0 + - - +
397P GLN* 3.3 25.9 + - + +
399P VAL* 1.3 77.5 - - - +
401P LYS* 1.3 57.0 + - - +
403P ALA* 3.3 0.7 + - - +
404P GLN* 2.9 63.7 + - - +
412P CYS* 3.8 31.6 + - + +
430P VAL* 5.6 0.2 - - - +
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Residues in contact with LYS 401 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397P GLN* 2.6 22.8 + - + +
398P THR* 4.0 4.3 - - - +
400P GLN* 1.3 73.9 - - - +
402P ALA* 1.3 63.8 + - - +
403P ALA 3.1 0.9 + - - -
404P GLN* 3.3 9.8 + - - +
405P ALA* 3.2 20.8 + - - +
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Residues in contact with ALA 402 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398P THR 3.5 13.9 + - - +
399P VAL 3.4 3.9 + - - +
401P LYS* 1.3 79.2 - - - +
403P ALA* 1.3 62.0 + - - +
405P ALA* 3.3 18.1 - - - +
406P PHE* 3.4 15.6 - - - -
447P LEU* 4.0 13.0 - - + -
450P SER* 4.2 8.3 + - - +
451P LEU* 4.0 4.7 - - + -
454P GLU* 3.8 23.3 - - - +
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Residues in contact with ALA 403 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399P VAL 2.8 19.8 + - - +
400P GLN* 3.4 7.9 - - - +
402P ALA* 1.3 74.0 - - - +
404P GLN* 1.3 54.0 + - - +
405P ALA 2.8 14.4 + - - -
406P PHE* 2.9 25.0 + - - -
410P LEU* 3.3 20.0 - - + +
412P CYS* 4.4 5.4 - - - -
432P ILE* 4.3 10.8 - - + -
443P ILE* 6.0 0.9 - - + -
447P LEU* 3.8 25.5 - - + +
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Residues in contact with GLN 404 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400P GLN* 2.9 57.4 + - + +
401P LYS* 3.9 7.8 - - - +
403P ALA* 1.3 73.5 - - + +
405P ALA* 1.3 56.8 + - - +
406P PHE 2.9 6.9 + - - -
407P ASN 3.1 28.4 + - - +
408P SER* 3.4 17.5 + - - +
410P LEU* 3.6 30.0 - - + +
412P CYS* 5.0 1.3 - - - -
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Residues in contact with ALA 405 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401P LYS 3.2 10.8 + - - +
402P ALA* 3.3 20.9 - - - +
403P ALA 2.8 0.4 + - - -
404P GLN* 1.3 78.2 - - - +
406P PHE* 1.3 65.4 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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