Contacts of the helix formed by residues 403 - 421 (chain D) in PDB entry 3HB0
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 GLY 403 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D GLY 3.1 15.4 + - - +
400D GLY 4.5 1.9 - - - -
401D LEU 3.3 3.2 + - - -
402D ILE* 1.3 80.2 - - - +
404D THR* 1.3 60.3 + - - -
405D PRO* 3.6 5.8 - - - -
406D LYS 3.6 0.8 + - - -
407D ARG* 2.9 29.5 + - - +
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Residues in contact with THR 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D GLY 4.4 0.6 + - - -
403D GLY* 1.3 68.1 - - - -
405D PRO* 1.3 79.7 - - + +
407D ARG* 3.0 22.5 + - - +
408D GLU* 3.5 19.8 + - + +
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Residues in contact with PRO 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403D GLY* 3.7 4.0 - - - -
404D THR* 1.3 99.4 - - + +
406D LYS* 1.3 72.4 + - + +
407D ARG 3.2 0.2 + - - -
408D GLU* 3.4 14.2 + - + +
409D THR* 3.4 15.1 + - - -
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Residues in contact with LYS 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D GLU* 5.5 1.2 + - - -
311D MET* 3.4 14.3 - - + +
314D ASN* 3.9 28.0 + - + +
319D HIS* 6.5 1.3 - - + -
402D ILE* 3.3 43.3 - - + +
403D GLY 3.9 0.7 - - - +
404D THR 3.3 0.4 - - - -
405D PRO* 1.3 83.8 - - + +
407D ARG* 1.3 65.1 + - - +
409D THR* 3.5 7.6 + - - -
410D TRP* 3.0 24.8 + - - +
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Residues in contact with ARG 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C LEU* 4.3 9.3 - - - +
306C LEU* 3.7 10.8 - - - +
309C GLU* 2.8 41.8 + - - -
399D GLY* 3.7 28.7 - - - +
402D ILE* 4.1 7.9 - - - -
403D GLY 2.9 16.1 + - - +
404D THR* 3.0 15.2 + - - +
406D LYS* 1.3 76.6 - - - +
408D GLU* 1.3 61.7 + - + +
410D TRP* 3.0 16.4 + - + +
411D LEU* 2.8 50.8 + - + +
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Residues in contact with GLU 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C VAL* 5.0 1.4 - - - +
306C LEU* 3.8 34.1 - - + +
404D THR* 4.0 21.1 - - + +
405D PRO* 3.4 8.4 + - - +
407D ARG* 1.3 78.8 - - + +
409D THR* 1.3 57.8 + - - +
411D LEU* 3.8 8.4 - - - +
412D GLN* 2.8 33.5 + - - +
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Residues in contact with THR 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D MET* 4.7 19.6 - - + +
311D MET* 4.5 12.6 - - + -
405D PRO 3.4 12.3 + - - -
406D LYS* 3.8 11.2 - - - -
407D ARG 3.2 0.6 - - - -
408D GLU* 1.3 78.2 - - - +
410D TRP* 1.3 58.5 + - - +
412D GLN* 3.7 6.0 - - - +
413D LEU* 3.0 27.9 + - + +
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Residues in contact with TRP 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D MET* 5.2 4.5 - - - -
311D MET* 3.5 25.3 - - + +
398D VAL* 3.7 36.6 - - + -
399D GLY 4.6 5.6 - - - -
402D ILE* 4.1 5.8 - - + -
406D LYS 3.0 14.5 + - - +
407D ARG* 3.0 27.6 + - + +
409D THR* 1.3 75.3 - - - +
411D LEU* 1.3 88.7 + - + +
413D LEU* 3.3 1.7 + - + +
414D ARG* 2.9 55.8 + - + +
459D LEU 4.3 3.4 - - - -
460D LEU* 3.0 55.1 + - + +
462D GLY* 5.1 1.3 - - - -
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Residues in contact with LEU 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C LEU* 3.8 36.7 - - + +
287C THR* 5.6 1.8 - - + -
302C VAL* 4.0 10.9 - - + +
306C LEU* 4.0 21.3 - - + -
407D ARG* 2.8 55.1 + - + +
408D GLU* 3.8 5.6 - - - +
410D TRP* 1.3 97.5 - - + +
412D GLN* 1.3 66.4 + - - +
414D ARG* 3.9 6.2 - - + +
415D ALA* 3.0 26.3 + - - +
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Residues in contact with GLN 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C THR* 3.8 6.9 + - - -
299C THR* 3.2 49.6 + - + +
302C VAL* 3.4 30.2 - - - +
303C ARG* 4.8 1.0 - - - +
408D GLU 2.8 18.9 + - - +
409D THR* 3.7 7.2 - - - +
411D LEU* 1.3 79.0 - - - +
413D LEU* 1.3 61.2 + - - +
415D ALA* 3.5 0.9 + - - +
416D GLU* 3.3 29.7 + - - +
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Residues in contact with LEU 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D ILE* 4.1 21.5 - - + +
307D MET* 3.8 44.4 - - + +
308D MET* 3.6 46.7 - - + +
311D MET* 4.1 14.4 - - - -
409D THR 3.0 17.8 + - - +
410D TRP* 3.6 5.2 - - + +
411D LEU 3.2 0.2 - - - -
412D GLN* 1.3 73.6 - - - +
414D ARG* 1.3 66.0 + - - +
415D ALA 3.0 1.7 + - - -
416D GLU* 3.1 16.3 + - - +
417D LEU* 3.0 22.1 + - - +
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Residues in contact with ARG 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C LEU 5.8 0.2 - - - +
287C THR* 4.4 31.2 + - - +
308D MET* 5.2 9.2 - - - -
410D TRP* 2.9 47.8 + - + +
411D LEU* 3.9 7.9 - - + +
413D LEU* 1.3 78.1 - - + +
415D ALA* 1.3 57.3 + - - +
417D LEU* 3.6 17.4 - - + +
418D GLU* 3.1 34.6 + - - +
425D LEU* 3.1 31.9 - - - +
429D LEU* 5.6 4.4 - - - +
460D LEU 3.1 18.1 + - - +
461D TYR* 3.6 8.6 + - - +
462D GLY* 3.6 25.7 - - - +
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Residues in contact with ALA 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C THR 3.9 9.6 + - - -
288C GLY* 3.9 19.9 - - - +
298C THR* 3.7 22.3 - - - +
302C VAL* 3.8 20.4 - - + -
411D LEU 3.0 17.7 + - - +
412D GLN 3.7 4.9 - - - +
413D LEU 3.0 0.2 - - - -
414D ARG* 1.3 75.8 - - - +
416D GLU* 1.3 65.2 + - - +
418D GLU* 3.3 4.2 + - - +
419D ALA 3.2 15.6 + - - -
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Residues in contact with GLU 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C THR* 4.1 19.7 + - - +
299C THR* 5.8 1.6 - - - +
300D THR* 5.0 2.4 - - - +
303D ARG* 2.6 43.7 + - - -
304D ILE* 3.8 15.0 - - + +
307D MET* 5.4 1.4 - - - +
412D GLN* 3.3 22.5 + - - +
413D LEU* 3.1 15.4 + - - +
415D ALA* 1.3 74.8 - - - +
417D LEU* 1.3 62.5 + - - +
419D ALA* 2.9 5.5 + - - +
420D LEU* 2.8 29.3 + - - +
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Residues in contact with LEU 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D ILE* 4.1 5.2 - - + +
285D LEU* 3.8 27.6 - - + -
304D ILE* 4.2 13.4 - - + +
308D MET* 4.6 11.9 - - + -
413D LEU 3.0 14.2 + - - +
414D ARG* 3.6 17.0 - - - +
416D GLU* 1.3 79.8 - - - +
418D GLU* 1.3 60.1 + - - +
420D LEU* 3.2 7.0 + - + +
421D THR* 2.8 62.2 + - + +
425D LEU* 6.2 1.8 - - + -
461D TYR* 3.6 37.9 - - + +
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Residues in contact with GLU 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C THR 3.5 23.1 - - - +
288C GLY 4.1 10.5 - - - +
289C THR* 4.0 5.3 - - + +
292C SER* 2.8 15.5 + - - -
414D ARG* 3.1 19.5 + - - +
415D ALA 3.6 9.4 - - - +
416D GLU 3.2 0.4 - - - -
417D LEU* 1.3 80.3 - - - +
419D ALA* 1.3 60.4 + - - +
421D THR* 3.7 4.9 + - - -
422D ASP 3.3 1.2 + - - -
423D LEU* 3.0 39.7 + - - +
425D LEU* 3.0 36.9 + - - +
426D THR* 2.7 27.6 + - - -
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Residues in contact with ALA 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C SER* 3.4 19.1 + - - +
298C THR* 3.9 18.2 - - + -
296D LYS* 4.5 1.9 + - - -
415D ALA 3.2 8.6 + - - +
416D GLU* 2.9 9.2 + - - +
418D GLU* 1.3 76.5 - - - +
420D LEU* 1.3 66.8 + - - +
422D ASP* 3.3 19.2 + - - +
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Residues in contact with LEU 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D LEU* 4.0 15.3 - - + -
290D PHE* 3.7 17.9 - - + -
296D LYS* 3.0 55.5 + - + +
297D ASP* 4.9 2.9 - - + +
300D THR* 4.4 19.1 - - + -
301D SER* 3.7 27.1 - - - +
304D ILE* 4.2 16.2 - - + -
416D GLU 2.8 16.6 + - - +
417D LEU* 3.6 11.0 - - + +
419D ALA* 1.3 78.0 - - - +
421D THR* 1.3 56.4 + - - +
422D ASP* 3.4 0.4 - - - +
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Residues in contact with THR 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D ILE* 4.0 18.6 - - + -
290D PHE* 3.9 24.4 - - + -
417D LEU* 2.8 54.0 + - + +
418D GLU* 3.7 9.2 + - - -
420D LEU* 1.3 74.8 - - + +
422D ASP* 1.3 71.6 + - - +
423D LEU 3.3 0.3 + - - -
424D TRP* 3.3 30.5 + - - +
523D HIS* 3.6 12.3 - - - -
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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