Contacts of the helix formed by residues 405 - 421 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404C THR* 1.3 93.6 - - + +
406C LYS* 1.3 66.1 + - + +
408C GLU* 3.2 12.1 - - + +
409C THR* 3.2 21.9 + - - +
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Residues in contact with LYS 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C MET* 3.6 17.3 - - + +
314C ASN* 3.5 36.5 + - - +
319C HIS* 6.3 1.8 - - + -
402C ILE* 3.7 44.0 - - + +
403C GLY 3.8 4.7 - - - +
404C THR 3.3 4.1 - - - -
405C PRO* 1.3 83.0 - - + +
407C ARG* 1.3 65.9 + - - +
409C THR* 3.3 3.8 + - - -
410C TRP* 2.9 25.1 + - - +
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Residues in contact with ARG 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C GLY* 3.9 25.5 - - - +
402C ILE* 3.5 13.2 - - + +
403C GLY 2.9 18.9 + - - +
404C THR* 4.8 2.5 - - - +
405C PRO 3.4 0.4 - - - -
406C LYS* 1.3 77.6 - - - +
408C GLU* 1.3 89.2 + - - +
410C TRP* 3.3 10.8 + - + +
411C LEU* 2.9 54.1 + - + +
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Residues in contact with GLU 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C THR* 3.1 36.2 + - - +
405C PRO* 3.2 16.7 - - + +
407C ARG* 1.3 106.4 + - - +
409C THR* 1.3 66.6 + - - +
411C LEU* 3.3 6.9 + - - +
412C GLN* 3.0 36.3 + - + +
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Residues in contact with THR 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C MET* 4.0 24.7 - - + +
311C MET* 4.7 13.2 - - + -
405C PRO* 3.2 14.0 + - - +
406C LYS* 3.3 10.4 + - - -
408C GLU* 1.3 78.3 - - - +
410C TRP* 1.3 52.4 + - - +
412C GLN* 3.4 16.1 + - - +
413C LEU* 2.8 35.1 + - + +
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Residues in contact with TRP 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C MET* 5.0 4.7 - - + -
311C MET* 3.7 22.8 - - + +
398C VAL* 3.9 26.9 - - + -
399C GLY* 4.1 20.9 - - - -
402C ILE* 5.0 5.2 - - + -
406C LYS 2.9 17.9 + - - +
407C ARG* 3.3 24.2 - - + +
409C THR* 1.3 76.1 - - - +
411C LEU* 1.3 82.4 + - + +
413C LEU* 3.4 3.6 + - + +
414C ARG* 3.0 52.7 + - + +
459C LEU 4.6 2.0 - - - -
460C LEU* 3.0 54.2 + - + +
462C GLY* 5.4 3.1 - - - -
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Residues in contact with LEU 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C ARG* 2.9 57.2 + - - +
408C GLU* 3.3 5.8 + - + +
410C TRP* 1.3 100.2 - - + +
412C GLN* 1.3 66.8 + - + +
414C ARG* 3.5 6.7 + - + +
415C ALA* 3.1 22.7 + - - +
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Residues in contact with GLN 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C GLU* 3.0 23.5 + - + +
409C THR* 3.6 16.6 + - - +
411C LEU* 1.3 76.8 - - + +
413C LEU* 1.3 64.1 + - - +
415C ALA* 3.2 9.3 + - - +
416C GLU* 3.0 31.6 + - + +
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Residues in contact with LEU 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C ILE* 3.8 27.8 - - + +
307C MET* 3.7 41.7 - - + -
308C MET* 3.7 41.7 - - + +
311C MET* 4.0 20.2 - - - -
409C THR 2.8 18.3 + - - +
410C TRP* 3.6 7.2 - - + +
411C LEU 3.2 0.2 - - - -
412C GLN* 1.3 76.3 - - - +
414C ARG* 1.3 58.1 + - + +
416C GLU* 3.0 11.4 + - - +
417C LEU* 2.8 28.6 + - + +
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Residues in contact with ARG 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C MET* 5.3 7.6 - - - -
410C TRP* 3.0 42.4 + - + +
411C LEU* 3.8 8.5 - - + +
413C LEU* 1.3 78.1 - - + +
415C ALA* 1.3 57.3 + - - +
417C LEU* 3.3 15.2 + - - +
418C GLU* 2.8 43.9 + - - +
425C LEU* 3.4 32.5 - - - +
429C LEU* 5.6 2.2 - - - +
460C LEU 3.1 23.2 + - - -
461C TYR* 3.5 25.5 + - - +
462C GLY* 4.2 5.1 - - - +
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Residues in contact with ALA 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C LEU 3.1 14.6 + - - +
412C GLN* 3.2 12.6 - - - +
413C LEU 3.1 0.2 - - - -
414C ARG* 1.3 74.7 - - - +
416C GLU* 1.3 67.1 + - + +
418C GLU* 3.3 6.8 + - - +
419C ALA* 3.2 22.2 + - - +
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Residues in contact with GLU 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C THR* 4.9 2.9 - - + +
303C ARG* 2.7 38.8 + - - -
304C ILE* 3.5 18.7 - - + +
307C MET* 4.9 4.0 - - - +
412C GLN* 3.0 19.9 + - + +
413C LEU* 3.0 15.9 + - - +
415C ALA* 1.3 76.1 - - + +
417C LEU* 1.3 56.4 + - - +
419C ALA* 3.4 7.2 + - - +
420C LEU* 3.0 29.0 + - - +
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Residues in contact with LEU 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ILE* 4.2 4.9 - - + +
285C LEU* 3.3 35.9 - - + -
304C ILE* 3.3 20.4 - - + +
308C MET* 5.5 6.5 - - + -
413C LEU* 2.8 13.0 + - + +
414C ARG* 3.4 20.6 - - - +
416C GLU* 1.3 73.7 - - - +
418C GLU* 1.3 68.9 + - + +
419C ALA 3.0 2.0 + - - -
420C LEU* 3.1 4.6 + - + -
421C THR* 2.8 40.5 + - + +
425C LEU* 6.0 3.4 - - + -
461C TYR* 3.5 37.5 - - + +
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Residues in contact with GLU 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414C ARG* 2.8 33.0 + - - +
415C ALA* 3.3 6.5 + - - +
417C LEU* 1.3 76.9 - - + +
419C ALA* 1.3 60.9 + - - +
421C THR* 3.6 6.5 + - - -
422C ASP* 3.1 2.6 + - - -
423C LEU* 2.7 57.3 + - + +
424C TRP 3.9 0.2 + - - -
425C LEU* 3.3 34.6 + - - +
426C THR* 2.8 27.7 + - - +
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Residues in contact with ALA 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C LYS* 4.0 3.6 - - - -
415C ALA 3.2 12.4 + - - +
416C GLU* 3.5 11.4 - - - +
417C LEU 3.0 0.4 - - - -
418C GLU* 1.3 75.3 - - - +
420C LEU* 1.3 65.8 + - - +
422C ASP* 3.2 21.0 + - - +
423C LEU* 5.4 2.0 - - - -
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Residues in contact with LEU 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C LEU* 3.9 26.9 - - + -
290C PHE* 3.4 19.3 - - + -
291C ALA* 4.9 0.7 - - + -
296C LYS* 3.3 51.9 + - + +
297C ASP* 4.2 6.7 - - + +
300C THR* 3.8 20.9 - - + -
301C SER* 3.8 34.8 - - - +
304C ILE* 4.9 4.5 - - + -
416C GLU 3.0 18.4 + - - +
417C LEU* 3.1 4.9 + - + +
419C ALA* 1.3 76.0 - - - +
421C THR* 1.3 57.6 + - + +
422C ASP 3.1 1.6 + - - -
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Residues in contact with THR 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ILE* 3.8 32.3 - - + -
285C LEU* 4.3 8.5 - - + -
290C PHE* 3.3 21.0 - - + -
417C LEU* 2.8 38.7 + - + +
418C GLU* 3.5 13.7 + - - -
420C LEU* 1.3 75.9 - - + +
422C ASP* 1.3 66.0 + - - +
423C LEU 3.2 0.3 + - - -
424C TRP* 3.2 22.2 + - - +
523C HIS* 3.1 18.0 + - - -
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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