Contacts of the helix formed by residues 405 - 421 (chain A) in PDB entry 3HB1
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 PRO 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A THR* 1.3 92.5 - - + +
406A LYS* 1.3 70.4 + - + +
407A ARG 3.2 3.0 + - - -
408A GLU* 3.3 16.4 + - + +
409A THR* 3.4 15.4 + - - +
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Residues in contact with LYS 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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310A GLU* 5.1 2.0 + - - +
311A MET* 3.4 14.4 - - + +
314A ASN* 3.3 39.9 + - - +
318A THR* 6.5 0.7 - - - -
319A HIS* 6.3 1.8 - - + -
402A ILE* 3.9 31.4 - - + +
403A GLY 3.4 10.1 + - - +
404A THR 5.6 0.2 - - - -
405A PRO* 1.3 84.3 - - + +
407A ARG* 1.3 62.6 + - - +
409A THR* 3.2 7.9 + - - -
410A TRP* 2.9 24.1 + - - +
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Residues in contact with ARG 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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399A GLY* 3.8 33.3 - - - +
402A ILE* 3.9 10.8 - - - -
403A GLY 3.0 18.2 + - - +
404A THR* 4.6 4.9 - - - -
405A PRO 3.2 0.6 - - - -
406A LYS* 1.3 76.8 - - - +
408A GLU* 1.3 100.8 + - - +
410A TRP* 3.3 6.1 - - + +
411A LEU* 3.0 51.8 + - + +
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Residues in contact with GLU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A THR* 3.1 34.1 + - - +
405A PRO* 3.3 12.1 - - + +
406A LYS 3.2 0.2 - - - -
407A ARG* 1.3 109.6 + - - +
409A THR* 1.3 66.2 + - - +
410A TRP 3.1 0.2 - - - -
411A LEU* 3.3 8.0 + - + +
412A GLN* 3.1 36.7 + - + +
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Residues in contact with THR 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A MET* 6.0 7.2 - - + -
311A MET* 4.2 16.8 - - + -
405A PRO* 3.4 12.8 + - - +
406A LYS* 3.2 11.8 + - - -
408A GLU* 1.3 77.6 - - - +
410A TRP* 1.3 57.0 + - - +
412A GLN* 3.5 11.8 + - - +
413A LEU* 2.9 31.4 + - + +
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Residues in contact with TRP 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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308A MET* 5.0 4.9 - - - -
311A MET* 3.8 22.2 - - + +
398A VAL* 3.8 26.0 - - + -
399A GLY* 4.0 21.3 - - - -
402A ILE* 4.0 16.4 - - + -
406A LYS 2.9 12.7 + - - +
407A ARG* 3.3 13.5 - - + +
409A THR* 1.3 75.3 - - - +
411A LEU* 1.3 87.3 + - + +
413A LEU* 3.1 2.4 + - + +
414A ARG* 2.8 66.9 + - + +
459A LEU 4.3 2.9 - - - -
460A LEU* 2.8 45.8 + - + +
462A GLY* 5.0 1.8 - - - -
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Residues in contact with LEU 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 ARG* 3.0 57.1 + - + +
408A GLU* 3.3 8.0 + - + +
410A TRP* 1.3 102.8 - - + +
412A GLN* 1.3 58.8 + - + +
414A ARG* 3.7 7.9 + - + +
415A ALA* 3.2 26.0 + - - +
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Residues in contact with GLN 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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408A GLU* 3.1 23.1 + - + +
409A THR* 3.7 11.6 + - - +
411A LEU* 1.3 75.2 - - + +
413A LEU* 1.3 61.6 + - - +
415A ALA* 3.3 6.9 + - - +
416A GLU* 2.9 38.1 + - + +
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Residues in contact with LEU 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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304A ILE* 4.0 26.5 - - + +
307A MET* 3.8 34.3 - - + -
308A MET* 3.7 41.1 - - + +
311A MET* 3.8 24.2 - - - -
409A THR* 2.9 20.7 + - + +
410A TRP* 3.5 5.6 - - + +
412A GLN* 1.3 77.4 - - - +
414A ARG* 1.3 54.1 + - + +
416A GLU* 3.0 11.6 + - - +
417A LEU* 2.8 37.3 + - + +
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Residues in contact with ARG 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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308A MET* 5.0 11.0 - - - -
410A TRP* 2.8 51.8 + - + +
411A LEU* 3.8 10.3 - - + +
413A LEU* 1.3 77.0 - - + +
415A ALA* 1.3 56.4 + - - +
417A LEU* 3.8 10.5 - - - +
418A GLU* 2.9 31.8 + - - +
425A LEU* 3.1 34.4 - - - +
429A LEU* 5.7 2.0 - - - +
460A LEU 2.9 27.5 + - - -
461A TYR* 3.7 22.5 + - - +
462A GLY* 3.7 4.8 - - - +
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Residues in contact with ALA 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 LEU 3.2 17.8 + - - +
412A GLN* 3.5 7.6 - - - +
413A LEU 3.1 0.6 - - - -
414A ARG* 1.3 75.9 - - - +
416A GLU* 1.3 64.7 + - + +
418A GLU* 3.5 5.5 + - - +
419A ALA* 3.2 22.7 + - - +
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Residues in contact with GLU 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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300A THR* 4.7 3.3 - - + +
303A ARG* 2.5 36.0 + - - -
304A ILE* 3.8 16.7 - - + +
307A MET* 4.9 3.1 - - - +
412A GLN* 2.9 23.0 + - + +
413A LEU* 3.4 16.5 - - - +
415A ALA* 1.3 75.8 - - + +
417A LEU* 1.3 64.5 + - - +
419A ALA* 3.2 7.5 + - - +
420A LEU* 3.1 23.3 + - - +
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Residues in contact with LEU 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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281A ILE* 3.8 5.2 - - + +
285A LEU* 3.4 31.4 - - + -
304A ILE* 3.7 17.0 - - + +
308A MET* 4.5 9.6 - - + -
413A LEU 2.8 15.6 + - - +
414A ARG* 3.8 13.2 - - - +
416A GLU* 1.3 79.4 - - - +
418A GLU* 1.3 70.0 + - - +
419A ALA 3.2 0.2 + - - -
420A LEU* 3.3 4.1 + - - +
421A THR* 2.8 49.5 + - + +
425A LEU* 5.6 4.5 - - + -
461A TYR* 3.6 37.7 - - + +
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Residues in contact with GLU 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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414A ARG* 2.9 19.3 + - - +
415A ALA* 3.9 7.0 - - - +
416A GLU 3.3 0.2 - - - -
417A LEU* 1.3 82.0 - - - +
419A ALA* 1.3 59.4 + - - +
421A THR* 3.3 6.4 + - - -
422A ASP 3.3 1.7 + - - -
423A LEU* 2.9 59.9 + - + +
425A LEU* 3.5 23.6 - - - +
426A THR* 2.7 40.2 + - - +
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Residues in contact with ALA 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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296A LYS* 4.0 3.5 + - - -
415A ALA 3.2 11.9 + - - +
416A GLU* 3.6 9.6 - - - +
417A LEU 3.1 0.4 - - - -
418A GLU* 1.3 77.1 - - - +
420A LEU* 1.3 65.1 + - - +
422A ASP* 3.2 21.6 + - - +
423A LEU* 5.3 3.1 - - - -
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Residues in contact with LEU 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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285A LEU* 3.9 27.4 - - + -
290A PHE* 3.3 23.5 - - + -
291A ALA* 5.3 0.4 - - - -
296A LYS* 3.4 39.1 - - + +
297A ASP 4.4 5.6 - - - +
300A THR* 4.0 18.8 - - + -
301A SER* 3.9 34.5 - - - +
304A ILE* 5.1 6.7 - - + -
416A GLU 3.1 16.3 + - - +
417A LEU* 3.3 5.8 + - - +
419A ALA* 1.3 78.0 - - - +
421A THR* 1.3 58.8 + - + +
422A ASP 3.2 0.4 - - - -
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Residues in contact with THR 421 (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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281A ILE* 3.8 32.3 - - + -
285A LEU* 4.4 1.3 - - + -
290A PHE* 3.4 19.4 - - + -
417A LEU* 2.8 35.0 + - + +
418A GLU* 3.3 14.2 + - - -
420A LEU* 1.3 83.8 - - + +
422A ASP* 1.3 66.4 + - - +
424A TRP* 3.2 22.7 + - - +
425A LEU 4.9 0.3 + - - -
523A HIS* 2.9 19.1 + - - -
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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
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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