Contacts of the helix formed by residues 408 - 418 (chain X) in PDB entry 4HSC
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 ASP 408 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389X PHE* 4.2 0.2 - - - -
406X THR* 3.0 16.4 + - - +
407X LYS* 1.3 79.8 - - - +
409X PHE* 1.3 62.8 + - - +
410X ASP* 2.9 35.0 + - - +
411X VAL* 2.9 35.6 + - + +
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Residues in contact with PHE 409 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350X VAL* 4.3 3.4 - - + -
352X LEU* 3.6 25.4 - - + -
368X ALA* 3.1 28.5 - - + -
369X LEU* 3.8 32.1 - - + -
374X VAL* 6.4 0.4 - - + -
384X LEU* 6.0 1.3 - - + -
389X PHE* 3.8 36.3 - + + -
407X LYS 3.6 4.6 + - - -
408X ASP* 1.3 72.3 + - - +
410X ASP* 1.3 58.2 + - - +
411X VAL 3.2 0.2 - - - -
412X ILE* 3.1 26.1 + - + -
413X ARG* 3.0 51.0 + - + +
416X ILE* 5.5 2.7 - - + -
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Residues in contact with ASP 410 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372X THR* 3.9 12.5 - - - +
408X ASP* 2.9 22.8 + - - +
409X PHE* 1.3 75.8 - - - +
411X VAL* 1.3 64.8 + - - +
413X ARG* 3.2 22.5 + - - +
414X ASN* 3.1 31.8 + - - +
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Residues in contact with VAL 411 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404X VAL* 4.4 16.4 - - + -
406X THR* 3.9 22.9 - - + +
408X ASP* 2.9 33.9 + - + +
410X ASP* 1.3 79.3 - - + +
412X ILE* 1.3 61.2 + - + +
414X ASN* 3.4 9.3 + - - +
415X VAL* 3.1 27.7 + - + +
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Residues in contact with ILE 412 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350X VAL* 3.7 35.0 - - + -
389X PHE* 3.7 26.2 - - + -
390X THR 4.0 2.5 - - - +
391X ALA* 3.7 31.4 - - + +
404X VAL* 4.8 1.8 - - + +
406X THR* 3.5 24.2 - - + -
409X PHE* 3.1 28.0 + - + +
410X ASP 3.1 0.4 - - - -
411X VAL* 1.3 78.4 - - + +
413X ARG* 1.3 65.0 + - - +
415X VAL* 3.2 6.3 + - + +
416X ILE* 3.1 28.4 + - + +
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Residues in contact with ARG 413 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368X ALA 2.8 29.3 + - - -
369X LEU 4.0 5.9 + - - -
370X LYS 4.8 0.2 + - - -
371X GLY* 3.1 34.1 + - - +
372X THR* 3.3 33.2 - - - +
374X VAL* 3.8 11.7 - - - +
409X PHE* 3.0 32.8 + - + +
410X ASP* 3.2 17.8 + - - +
412X ILE* 1.3 75.1 - - - +
414X ASN* 1.3 63.5 + - - +
416X ILE* 3.5 11.5 + - + +
417X LYS* 3.0 28.6 + - - +
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Residues in contact with ASN 414 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410X ASP* 3.1 17.3 + - - +
411X VAL* 3.8 10.4 - - - +
413X ARG* 1.3 79.2 - - - +
415X VAL* 1.3 59.3 + - + +
417X LYS* 4.3 15.7 + - - +
418X ASP* 2.8 46.2 + - - +
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Residues in contact with VAL 415 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348X VAL* 4.4 6.5 - - + +
391X ALA* 4.0 26.2 - - + +
393X VAL* 3.5 31.0 - - + -
404X VAL* 4.9 15.7 - - + -
411X VAL* 3.1 25.5 + - + +
412X ILE* 3.2 6.9 + - + +
414X ASN* 1.3 79.3 - - + +
416X ILE* 1.3 63.1 + - - +
418X ASP* 3.3 5.7 + - - -
419X ASN* 2.8 28.6 + - - +
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Residues in contact with ILE 416 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297X TYR* 3.4 57.2 - - + +
299X GLN* 4.0 14.7 + - - +
348X VAL* 4.3 18.1 - - + +
350X VAL* 4.1 4.5 - - + -
369X LEU* 5.1 3.4 - - + -
409X PHE* 5.5 3.1 - - + -
412X ILE* 3.1 28.6 + - + +
413X ARG* 3.6 10.5 - - + +
415X VAL* 1.3 76.4 - - - +
417X LYS* 1.3 65.6 + - + +
419X ASN* 3.1 14.2 + - - +
420X ALA* 3.4 12.4 + - + +
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Residues in contact with LYS 417 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413X ARG 3.0 15.1 + - - +
414X ASN* 3.3 16.5 + - - +
416X ILE* 1.3 82.1 - - - +
418X ASP* 1.3 66.6 + - - +
419X ASN 3.0 5.9 + - - -
420X ALA* 3.2 19.7 + - - +
421X THR* 4.5 6.9 + - - +
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Residues in contact with ASP 418 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414X ASN* 2.8 33.5 + - - +
415X VAL* 4.0 6.1 - - - +
416X ILE 3.3 0.4 - - - -
417X LYS* 1.3 83.9 - - - +
419X ASN* 1.3 64.3 + - - +
420X ALA 3.5 0.4 - - - -
421X THR* 4.7 5.8 + - - -
426X ASN* 3.7 20.3 + - - +
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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