Contacts of the helix formed by residues 400 - 412 (chain C) in PDB entry 3HYW
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 400 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388C TYR* 3.9 10.5 - - - +
391C TRP* 4.8 4.9 - - + -
392C LYS* 3.7 13.9 - - + -
397C ASN* 3.6 24.4 - - + +
398C ILE 3.5 8.1 - - - +
399C ALA* 1.3 89.5 - - - +
401C SER* 1.3 66.9 - - - +
402C PHE* 3.5 26.5 - - + -
403C GLU* 3.0 26.9 + - - +
404C GLU* 3.9 3.1 + - - +
391D TRP* 3.7 20.4 - - + +
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Residues in contact with SER 401 (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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397C ASN* 5.0 0.6 - - - +
399C ALA 3.4 3.3 + - - -
400C PRO* 1.3 71.8 - - - +
402C PHE* 1.3 65.9 + - - +
403C GLU 3.3 1.0 + - - -
404C GLU* 3.4 8.4 + - - +
405C LYS* 3.4 30.5 + - - +
387D LYS 5.5 0.3 + - - -
391D TRP* 3.2 10.4 - - - +
394D ARG* 4.7 2.3 + - - -
432D SO4 3.0 40.5 + - - -
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Residues in contact with PHE 402 (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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388C TYR* 3.5 28.0 - + - -
391C TRP* 5.6 0.7 - + - -
400C PRO* 3.1 20.6 + - + -
401C SER* 1.3 78.0 + - - +
403C GLU* 1.3 60.7 + - - +
405C LYS* 3.2 10.9 + - - +
406C VAL* 2.8 40.7 + - + +
500C DCQ 3.7 28.7 - - + -
387D LYS* 3.7 26.9 - - + +
388D TYR* 3.6 38.1 - + + +
391D TRP* 3.5 44.0 - + + -
402D PHE* 4.6 2.5 - + - -
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Residues in contact with GLU 403 (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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318C GLU* 3.6 5.5 - - - +
385C PHE* 5.1 0.2 - - - -
388C TYR* 2.5 38.1 + - - +
392C LYS* 2.7 28.3 + - - -
398C ILE 4.6 2.0 - - - -
399C ALA* 5.3 1.8 - - - -
400C PRO* 3.0 19.5 + - + +
402C PHE* 1.3 85.9 - - + +
404C GLU* 1.3 62.6 + - - +
406C VAL* 3.2 5.4 + - - +
407C LEU* 3.0 30.6 + - + +
500C DCQ 3.4 43.6 - - + +
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Residues in contact with GLU 404 (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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322C MET* 4.6 7.8 - - + +
400C PRO 3.9 2.7 + - - +
401C SER* 3.4 10.8 + - - +
402C PHE 3.4 0.4 - - - -
403C GLU* 1.3 77.5 - - - +
405C LYS* 1.3 59.1 + - + +
407C LEU* 3.5 9.0 + - - +
408C GLU* 2.9 34.0 + - - +
413C VAL 4.5 2.8 - - - +
414C HIS* 5.3 3.6 + - - -
415C PRO* 3.6 41.6 - - + +
416C ILE* 6.1 0.2 - - - +
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Residues in contact with LYS 405 (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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401C SER* 3.4 21.0 + - - +
402C PHE* 3.2 10.4 + - - +
404C GLU* 1.3 78.5 - - + +
406C VAL* 1.3 52.7 + - - +
408C GLU* 3.1 11.0 + - - +
409C ILE* 2.8 42.3 + - + +
387D LYS* 3.6 53.4 - - + +
394D ARG* 5.6 5.9 - - - +
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Residues in contact with VAL 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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402C PHE* 2.8 35.7 + - + +
403C GLU* 3.2 6.3 + - - +
405C LYS* 1.3 72.5 - - - +
407C LEU* 1.3 56.7 + - + +
409C ILE* 3.3 7.0 + - - +
410C PHE* 2.9 36.3 + - + +
500C DCQ 4.2 16.6 - - + -
600C LMT 3.8 43.5 - - + -
384D ALA* 3.7 31.4 - - + +
387D LYS* 5.3 1.8 - - + -
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Residues in contact with LEU 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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315C MET* 4.1 22.7 - - + -
346C ILE* 3.6 24.5 - - + -
403C GLU* 3.0 28.2 + - + +
404C GLU* 3.9 6.7 - - - +
406C VAL* 1.3 75.7 - - + +
408C GLU* 1.3 57.1 + - - +
410C PHE* 4.6 1.6 - - - +
411C LEU* 2.9 31.1 + - + +
412C LYS 3.3 5.2 + - - -
413C VAL* 3.3 20.4 + - + +
500C DCQ 3.8 39.0 - - + -
600C LMT 4.4 14.1 - - + -
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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 GLU* 2.9 24.7 + - + +
405C LYS* 3.4 10.4 - - - +
407C LEU* 1.3 76.3 - - - +
409C ILE* 1.3 67.7 + - - +
412C LYS* 3.0 25.4 + - - +
413C VAL 3.7 21.0 + - - +
414C HIS* 3.9 29.9 + - + +
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Residues in contact with ILE 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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405C LYS* 2.8 29.8 + - + +
406C VAL* 3.6 5.8 - - - +
408C GLU* 1.3 77.4 - - + +
410C PHE* 1.3 64.9 + - + +
412C LYS* 4.9 2.1 + - - +
380D TYR* 3.7 54.8 - - + +
383D THR* 3.8 29.8 - - + +
384D ALA* 4.0 19.1 - - - +
387D LYS* 4.2 13.7 - - + +
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Residues in contact with PHE 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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406C VAL* 2.9 32.2 + - + +
407C LEU* 4.6 0.9 - - - +
409C ILE* 1.3 83.5 - - + +
411C LEU* 1.3 68.9 + - + +
412C LYS* 3.8 6.4 + - - -
600C LMT 3.8 55.7 - - + +
377D TRP* 4.6 11.0 - + + -
380D TYR* 3.9 19.5 - + + -
381D PHE* 3.8 31.4 - + + -
384D ALA* 3.8 24.5 - - + -
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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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346C ILE* 3.5 38.6 - - + -
357C PHE* 4.9 2.0 - - + -
359C PHE* 3.9 29.1 - - + -
361C ASP* 5.3 0.9 - - - +
369C ARG* 4.6 8.9 + - - +
371C ILE* 3.6 30.3 - - + -
407C LEU* 2.9 15.6 + - + +
410C PHE* 1.3 86.2 - - + +
412C LYS* 1.3 78.7 + - - +
413C VAL* 3.1 14.5 + - + +
600C LMT 3.9 31.6 - - + -
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Residues in contact with LYS 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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435A SO4 4.5 8.8 + - - -
361C ASP* 5.2 5.5 - - - +
369C ARG* 3.8 47.7 + - - +
408C GLU* 3.0 21.9 + - - +
409C ILE 5.5 1.6 - - - +
410C PHE 5.1 6.1 + - - -
411C LEU* 1.3 80.9 - - - +
413C VAL* 1.3 62.3 + - - +
414C HIS* 3.5 17.2 + - + +
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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