Contacts of the helix formed by residues 423 - 437 (chain B) in PDB entry 3H11
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 423 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A ASP* 4.9 6.0 - - - +
421B GLY 3.5 2.8 + - - -
422B ASP* 1.3 76.8 - - - +
424B ILE* 1.3 63.7 + - - +
425B LEU* 3.0 18.9 + - - +
426B THR* 2.4 43.7 + - - -
427B ILE* 3.1 19.6 + - - +
458B LYS* 3.7 34.8 - - + +
459B LEU 3.2 15.3 + - - +
460B VAL* 3.9 3.4 - - - -
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Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B PHE* 4.7 10.3 - - + -
385B LEU* 3.9 23.1 - - + -
414B LEU* 3.9 11.9 - - + -
418B CYS* 3.9 20.9 - - - -
422B ASP 4.6 0.9 - - - +
423B ASP* 1.3 74.3 - - - +
425B LEU* 1.3 58.4 + - - +
427B ILE* 3.3 6.3 + - + +
428B LEU* 2.9 34.8 + - + +
459B LEU* 2.8 48.0 + - + +
460B VAL* 4.3 0.9 - - - -
461B PHE* 3.4 41.5 - - + +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LEU* 4.2 18.4 - - + +
444A ILE* 3.6 39.0 - - + -
469A HIS* 5.3 2.3 + - - +
385B LEU* 3.9 28.7 - - + -
423B ASP* 3.0 9.9 + - - +
424B ILE* 1.3 73.6 - - - +
426B THR* 1.3 67.9 + - - +
428B LEU* 3.1 19.8 + - + +
429B THR* 3.1 15.7 + - - -
451B PRO* 5.2 1.3 - - + -
453B PHE* 3.9 30.7 - - + -
455B LEU* 4.2 17.5 - - + -
457B LYS 5.6 1.3 - - - +
458B LYS* 6.4 1.1 - - - -
459B LEU* 4.9 4.0 + - + +
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Residues in contact with THR 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 3.7 35.7 - - + +
240A PRO* 4.0 11.1 - - + +
440A LEU* 6.1 1.1 - - - -
441A ASP* 4.6 8.7 + - - -
422B ASP* 4.8 4.7 - - - +
423B ASP* 2.4 38.9 + - - -
425B LEU* 1.3 76.4 - - - +
427B ILE* 1.3 62.2 + - - +
429B THR* 3.2 16.6 + - - -
430B GLU* 3.2 12.5 + - - +
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Residues in contact with ILE 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 3.9 20.9 - - + -
410B LEU* 5.0 3.1 - - + -
413B SER* 3.8 25.6 - - - +
414B LEU* 4.0 21.8 - - + +
417B ARG* 3.8 20.6 - - + -
418B CYS* 3.9 22.9 - - - +
422B ASP* 3.8 16.8 - - + +
423B ASP 3.1 14.2 + - - +
424B ILE* 3.4 12.3 - - + +
426B THR* 1.3 77.4 - - - +
428B LEU* 1.3 58.3 + - + +
430B GLU* 3.0 6.9 + - - +
431B VAL* 2.9 29.7 + - + +
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Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A HIS* 5.9 0.2 - - - +
341B PHE* 4.2 8.5 - - + -
385B LEU* 3.9 37.5 - - + -
387B GLY* 5.0 2.5 - - - -
406B TYR* 3.8 21.1 - - + +
410B LEU* 3.8 28.3 - - + -
424B ILE* 2.9 24.3 + - + +
425B LEU* 3.1 12.7 + - + +
427B ILE* 1.3 73.9 - - + +
429B THR* 1.3 60.2 + - - +
431B VAL* 3.3 8.6 + - + +
432B ASN* 2.9 31.8 + - - +
451B PRO* 3.9 27.4 - - + -
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Residues in contact with THR 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PRO* 3.6 22.7 - - + -
440A LEU* 4.7 5.9 - - - +
469A HIS* 3.6 19.1 + - - -
471A LEU* 3.6 20.9 - - + +
472A ARG 3.9 0.7 - - - -
473A LYS 3.8 22.9 - - - +
425B LEU 3.1 12.9 + - - -
426B THR* 3.2 10.7 + - - -
428B LEU* 1.3 75.9 - - - +
430B GLU* 1.3 64.0 + - - +
432B ASN* 3.1 10.6 + - - +
433B TYR* 3.0 21.5 + - - +
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Residues in contact with GLU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 3.7 32.8 - - + -
240A PRO* 3.3 7.3 - - + +
241A GLU* 2.7 53.1 + - - +
413B SER* 4.4 9.9 - - - +
417B ARG* 5.8 0.9 - - + -
426B THR 3.2 8.3 + - - +
427B ILE* 3.0 11.4 + - - +
429B THR* 1.3 81.6 - - - +
431B VAL* 1.3 56.3 + - - +
433B TYR* 3.3 11.6 + - - +
434B GLU* 2.9 51.7 + - - +
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B TYR* 3.7 36.3 - - + -
409B SER* 3.8 19.1 - - - +
410B LEU* 3.8 30.3 - - + +
413B SER* 3.9 17.9 - - - +
427B ILE* 2.9 19.5 + - + +
428B LEU* 3.6 13.5 - - + +
430B GLU* 1.3 74.7 - - - +
432B ASN* 1.3 67.3 + - - +
434B GLU* 4.4 0.4 - - - +
435B VAL* 2.9 29.1 + - + +
449B PRO* 4.8 0.4 - - + -
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Residues in contact with ASN 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A HIS* 3.8 14.6 - - - -
470A THR* 3.6 21.2 - - - +
471A LEU 2.9 25.8 + - - +
472A ARG* 4.6 0.7 - - - -
406B TYR* 5.6 0.3 - - - -
428B LEU 2.9 17.4 + - - +
429B THR 3.1 9.4 + - - +
431B VAL* 1.3 75.1 - - - +
433B TYR* 1.3 57.9 + - - +
436B SER* 3.0 32.7 + - - -
448B MET* 3.6 18.5 - - + +
449B PRO* 3.3 30.6 + - - +
451B PRO* 3.8 11.3 - - - +
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Residues in contact with TYR 433 (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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241A GLU* 3.6 41.0 + - + -
242A GLU* 3.2 37.0 + - + +
472A ARG* 3.3 50.2 - - + +
473A LYS* 4.9 3.6 - - + -
429B THR 3.0 7.9 + - - +
430B GLU* 3.4 20.2 - - - +
432B ASN* 1.3 75.1 - - - +
434B GLU* 1.3 65.9 + - + +
436B SER* 3.0 15.0 + - - -
437B ASN* 2.9 46.2 + - - -
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Residues in contact with GLU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLU* 4.3 7.8 - - - +
409B SER* 3.1 27.3 + - - +
412B GLN* 5.6 3.6 - - - +
413B SER* 3.8 16.2 + - - -
430B GLU* 2.9 43.0 + - - +
431B VAL 3.9 0.4 - - - +
433B TYR* 1.3 75.4 - - + +
435B VAL* 1.3 65.4 + - - +
437B ASN* 3.2 16.9 + - - +
438B LYS 3.4 12.5 + - - +
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Residues in contact with VAL 435 (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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405B TRP* 3.8 25.2 - - + +
406B TYR* 4.0 9.4 - - - -
409B SER* 3.8 25.1 - - - -
431B VAL* 2.9 28.3 + - + +
434B GLU* 1.3 72.7 - - - +
436B SER* 1.3 58.4 + - - +
438B LYS* 2.8 27.3 + - - +
446B LYS* 5.0 0.2 + - - -
447B GLN* 3.7 32.4 + - + +
449B PRO* 3.5 26.0 - - + -
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Residues in contact with SER 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A HIS* 5.9 3.1 - - - -
472A ARG* 3.5 28.1 + - - -
432B ASN 3.0 18.5 + - - -
433B TYR* 3.0 14.9 + - - -
435B VAL* 1.3 77.0 - - - +
437B ASN* 1.3 60.4 + - - +
438B LYS 3.3 1.1 - - - -
446B LYS* 3.2 29.6 - - - +
447B GLN 3.2 18.8 + - - +
448B MET* 4.4 9.0 - - - -
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Residues in contact with ASN 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ARG* 5.3 4.0 + - - -
433B TYR* 2.9 58.9 + - - +
434B GLU* 3.2 8.2 + - - +
435B VAL 3.0 0.6 - - - -
436B SER* 1.3 82.5 + - - +
438B LYS* 1.3 80.4 + - - +
446B LYS* 4.6 1.1 - - - +
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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