Contacts of the helix formed by residues 400 - 412 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A TRP* 3.4 37.2 - - + +
388B TYR* 3.2 24.7 - - + +
391B TRP* 5.7 1.1 - - + -
392B LYS* 3.7 14.1 - - + -
397B ASN* 3.5 14.8 - - - +
398B ILE 3.4 8.3 - - - +
399B ALA* 1.4 89.8 - - - +
401B SER* 1.3 65.9 + - - +
402B PHE* 3.2 13.2 - - + -
403B GLU* 3.0 22.6 + - + +
404B GLU* 3.8 3.8 + - - +
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Residues in contact with SER 401 (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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391A TRP* 3.4 8.0 - - - +
394A ARG* 3.8 7.8 + - - -
432A SO4 2.9 37.4 + - - -
397B ASN* 5.1 0.4 - - - +
399B ALA 3.5 4.2 + - - -
400B PRO* 1.3 72.1 - - - +
402B PHE* 1.3 64.0 + - - +
403B GLU 3.3 0.3 + - - -
404B GLU* 3.4 10.4 + - - +
405B LYS* 3.3 34.2 + - - +
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Residues in contact with PHE 402 (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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387A LYS* 3.6 31.0 - - + +
388A TYR* 3.5 35.2 - + + -
391A TRP* 3.6 37.0 - + + -
402A PHE* 5.5 0.4 - + - -
388B TYR* 3.3 30.3 - + - -
391B TRP* 6.1 0.2 - + - -
400B PRO* 3.2 23.6 - - + -
401B SER* 1.3 80.9 + - - +
403B GLU* 1.3 61.9 + - - +
405B LYS* 3.2 10.5 + - - +
406B VAL* 2.8 43.7 + - + +
500B DCQ 3.6 27.4 - - + -
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Residues in contact with GLU 403 (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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318B GLU* 3.8 10.5 - - - +
385B PHE* 5.0 0.3 - - - -
388B TYR* 2.6 33.5 + - - +
392B LYS* 2.8 28.4 + - - -
398B ILE 4.6 1.8 - - - -
399B ALA* 5.4 2.2 - - - -
400B PRO* 3.0 17.4 + - + +
402B PHE* 1.3 87.4 - - + +
404B GLU* 1.3 57.6 + - - +
406B VAL* 3.3 4.7 + - - +
407B LEU* 3.0 37.3 + - + +
500B DCQ 3.2 43.8 - - + +
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Residues in contact with GLU 404 (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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322B MET* 4.9 6.7 - - - +
400B PRO 3.8 4.4 + - - +
401B SER* 3.4 12.5 + - - +
403B GLU* 1.3 77.9 - - - +
405B LYS* 1.3 62.8 + - + +
407B LEU* 3.5 8.2 + - - +
408B GLU* 3.0 23.5 + - + +
413B VAL 4.4 2.3 - - - +
414B HIS* 5.7 2.3 + - - -
415B PRO* 3.6 42.1 - - + +
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Residues in contact with LYS 405 (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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387A LYS* 3.6 50.7 - - + +
394A ARG* 5.0 9.6 - - - +
401B SER* 3.3 27.6 - - - +
402B PHE* 3.2 9.1 + - - +
404B GLU* 1.3 79.0 - - + +
406B VAL* 1.3 61.9 + - - +
408B GLU* 3.2 7.6 + - - +
409B ILE* 3.0 30.7 + - + +
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Residues in contact with VAL 406 (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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384A ALA* 3.8 28.5 - - + +
387A LYS* 5.0 2.5 - - + -
402B PHE* 2.8 41.7 + - + +
403B GLU* 3.3 6.5 + - - +
405B LYS* 1.3 71.0 - - - +
407B LEU* 1.3 60.8 + - + +
409B ILE* 3.3 7.7 + - - +
410B PHE* 3.0 49.3 + - + +
500B DCQ 4.8 7.6 - - + -
600B LMT 3.7 33.2 - - + -
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Residues in contact with LEU 407 (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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315B MET* 3.7 22.2 - - + -
346B ILE* 4.2 12.8 - - + -
403B GLU* 3.0 27.8 + - + +
404B GLU* 3.9 7.0 - - - +
406B VAL* 1.3 77.8 - - + +
408B GLU* 1.3 61.4 + - - +
410B PHE* 5.0 0.9 - - - -
411B LEU* 2.9 33.8 + - + +
412B LYS 3.2 4.7 + - - -
413B VAL* 3.4 24.6 + - + +
500B DCQ 3.5 46.2 - - + -
600B LMT 5.2 7.4 - - + -
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Residues in contact with GLU 408 (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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404B GLU* 3.0 18.7 + - + +
405B LYS* 3.5 8.3 - - - +
407B LEU* 1.3 76.8 - - - +
409B ILE* 1.3 63.8 + - + +
412B LYS* 2.9 40.6 + - - +
413B VAL 3.5 12.8 + - - +
414B HIS* 2.8 42.2 + - + -
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Residues in contact with ILE 409 (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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380A TYR* 3.1 69.4 - - + +
383A THR* 4.2 17.9 - - + -
384A ALA* 4.1 10.5 - - + +
387A LYS* 6.0 4.7 - - + -
405B LYS* 3.0 20.1 + - + +
406B VAL* 3.3 12.5 + - - +
408B GLU* 1.3 83.0 - - + +
410B PHE* 1.3 73.5 + - + +
412B LYS* 5.0 4.2 + - - +
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Residues in contact with PHE 410 (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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377A TRP* 4.7 7.6 - - + -
380A TYR* 3.6 37.5 - + + -
381A PHE* 3.8 11.2 - + + -
384A ALA* 3.7 19.7 - - + -
406B VAL* 3.0 32.8 + - + +
407B LEU* 4.6 1.1 - - - +
409B ILE* 1.3 87.0 - - + +
411B LEU* 1.3 66.8 + - + +
412B LYS* 3.7 1.8 - - - +
600B LMT 3.6 63.9 - - + +
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Residues in contact with LEU 411 (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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346B ILE* 3.3 39.9 - - + -
357B PHE* 4.6 3.4 - - + -
359B PHE* 3.8 32.2 - - + -
361B ASP* 4.9 0.9 - - - +
369B ARG* 4.0 9.9 + - - +
371B ILE* 3.6 30.5 - - + -
407B LEU* 2.9 20.6 + - + +
410B PHE* 1.3 86.4 - - + +
412B LYS* 1.3 73.3 + - - +
413B VAL* 3.2 11.5 + - + -
600B LMT 4.2 28.7 - - + -
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Residues in contact with LYS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ASP* 4.3 8.5 - - - +
369B ARG* 3.8 31.2 + - - +
408B GLU* 2.9 34.6 + - - +
409B ILE 5.3 4.0 - - - +
410B PHE 5.4 0.9 - - - +
411B LEU* 1.3 80.9 - - - +
413B VAL* 1.3 60.5 + - - +
414B HIS* 3.7 12.2 + - - +
431B SO4 3.6 21.8 + - - +
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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