Contacts of the helix formed by residues 443 - 461 (chain C) in PDB entry 5HVO
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 SER 443 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441C SER 3.7 3.0 + - - -
442C MET* 1.3 78.3 - - - +
444C ASP* 1.3 57.9 + - - +
445C GLU* 3.3 20.9 - - - +
446C GLN* 3.0 27.0 + - - +
447C ARG* 2.9 27.4 + - - +
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Residues in contact with ASP 444 (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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403C LYS* 5.3 2.1 - - - +
442C MET 3.8 0.9 + - - -
443C SER* 1.3 73.1 - - - +
445C GLU* 1.3 68.2 + - - +
447C ARG* 3.5 19.1 + - - +
448C ALA* 2.9 29.6 + - - +
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Residues in contact with GLU 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C SER* 3.3 22.4 - - - +
444C ASP* 1.3 89.4 + - - +
446C GLN* 1.3 57.9 + - - +
448C ALA* 3.1 7.4 + - - +
449C ARG* 2.9 35.9 + - - +
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Residues in contact with GLN 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C GLU* 4.6 8.7 + - - +
442C MET* 3.2 32.5 - - + +
443C SER* 3.0 20.5 + - - +
445C GLU* 1.3 73.7 - - - +
447C ARG* 1.3 66.3 - - - +
449C ARG* 3.2 37.0 + - - +
450C LYS* 3.0 43.6 + - - +
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Residues in contact with ARG 447 (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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280C LYS* 4.2 15.2 - - - +
377C ASP* 3.9 28.1 + - - +
402C ARG* 3.1 39.4 + - - +
403C LYS* 3.1 27.1 + - + +
404C GLY* 3.6 10.9 - - - +
405C VAL* 3.9 11.9 - - + +
439C ALA 4.5 8.1 + - - -
440C VAL 5.9 0.2 - - - -
442C MET* 3.7 39.9 + - + -
443C SER 2.9 16.5 + - - +
444C ASP* 3.5 18.6 + - - +
446C GLN* 1.3 76.7 - - - +
448C ALA* 1.3 57.5 + - - +
450C LYS* 3.4 3.6 + - - +
451C PHE* 2.9 30.8 + - - +
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Residues in contact with ALA 448 (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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403C LYS* 4.1 28.2 - - + +
444C ASP 2.9 18.3 + - - +
445C GLU* 3.1 7.8 + - - +
447C ARG* 1.3 75.0 - - - +
449C ARG* 1.3 64.4 + - - +
451C PHE* 4.0 1.4 - - - +
452C GLU* 3.0 31.4 + - - +
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Residues in contact with ARG 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C SER* 5.5 0.4 + - - -
445C GLU* 2.9 15.2 + - - +
446C GLN* 3.2 50.5 + - - +
448C ALA* 1.3 79.1 - - - +
450C LYS* 1.3 68.2 + - + +
452C GLU* 3.4 10.6 + - - +
453C LYS* 3.4 29.3 + - - +
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Residues in contact with LYS 450 (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 VAL* 5.3 3.8 - - + -
420C GLY* 3.1 36.6 + - - +
421C SER 5.2 1.4 + - - -
422C LEU* 4.0 17.6 - - + +
438C GLU* 4.5 2.1 + - - -
442C MET* 3.7 39.5 - - + -
446C GLN* 3.0 34.9 + - + +
447C ARG* 3.9 3.4 - - - +
449C ARG* 1.3 80.5 - - + +
451C PHE* 1.3 63.8 + - - +
452C GLU 3.3 0.3 + - - -
453C LYS* 3.3 9.4 + - - +
454C LEU* 3.2 27.5 + - + +
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Residues in contact with PHE 451 (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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396C ILE* 3.4 32.1 - - + -
399C GLN* 3.4 21.3 - - + -
400C GLN* 3.4 43.1 - - + -
403C LYS* 3.7 39.0 - - + +
404C GLY 5.0 5.4 - - - +
447C ARG 2.9 18.3 + - - +
448C ALA 4.0 1.8 - - - +
450C LYS* 1.3 76.4 - - - +
452C GLU* 1.3 70.5 + - - +
454C LEU* 3.2 10.7 + - + +
455C TYR* 2.8 52.4 + + + +
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Residues in contact with GLU 452 (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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403C LYS* 4.0 18.5 + - - -
448C ALA* 3.0 24.3 + - - +
449C ARG* 3.6 6.7 - - - +
450C LYS 3.2 0.2 - - - -
451C PHE* 1.3 89.4 - - - +
453C LYS* 1.3 62.3 + - + +
455C TYR* 3.4 8.1 + - - +
456C LYS* 3.0 24.0 + - - +
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Residues in contact with LYS 453 (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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419C ASN* 3.6 39.1 + - + +
420C GLY* 4.8 5.7 - - - -
449C ARG* 3.4 24.0 + - - +
450C LYS* 3.3 7.2 + - - +
452C GLU* 1.3 78.9 - - + +
454C LEU* 1.3 63.2 + - - +
456C LYS* 3.2 18.6 + - - +
457C TYR* 3.1 20.8 + - - +
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Residues in contact with LEU 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C ILE* 3.8 35.2 - - + -
404C GLY 5.7 3.4 - - - +
406C LEU* 4.5 15.3 - - + +
418C LEU* 3.6 34.8 - - + +
419C ASN 3.2 20.0 - - - +
420C GLY 4.0 15.0 - - - +
421C SER* 4.0 5.4 - - - +
450C LYS* 3.2 18.6 + - + +
451C PHE* 3.2 12.2 + - + +
453C LYS* 1.3 76.0 - - - +
455C TYR* 1.3 63.2 + - - +
457C TYR* 3.2 6.2 + - - +
458C ILE* 3.0 28.6 + - - +
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Residues in contact with TYR 455 (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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253C PRO* 5.0 6.7 - - + +
257C THR* 3.6 16.8 - - - +
396C ILE* 3.8 10.5 - - + +
397C ALA* 3.9 23.1 - - + -
400C GLN* 3.1 46.0 + - + -
451C PHE* 2.8 45.4 + + + +
452C GLU* 4.0 9.2 - - - +
454C LEU* 1.3 73.4 - - - +
456C LYS* 1.3 57.1 + - - +
458C ILE* 4.0 15.5 - - + -
459C SER* 2.5 47.9 + - - -
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Residues in contact with LYS 456 (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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478A SER* 5.9 7.0 - - - +
452C GLU 3.0 14.1 + - - +
453C LYS* 3.4 19.6 - - - +
454C LEU 3.2 0.2 - - - -
455C TYR* 1.3 78.1 - - - +
457C TYR* 1.3 64.4 + - - +
459C SER* 3.2 13.2 + - - -
460C LYS* 3.4 17.2 - - + +
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Residues in contact with TYR 457 (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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248C PRO* 4.2 18.5 + - - +
249C ILE 5.1 1.7 + - - -
388C MET* 6.1 0.2 - - - -
393C PHE* 3.7 22.7 - + - -
417C SER* 3.3 50.5 + - - +
418C LEU* 3.8 16.8 - - + -
419C ASN 5.9 0.4 - - - +
453C LYS 3.1 12.4 + - - +
454C LEU* 3.2 9.4 + - - +
456C LYS* 1.3 78.4 - - - +
458C ILE* 1.3 63.4 + - - +
460C LYS* 3.1 2.2 + - - -
461C TYR* 2.8 82.2 + + + +
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Residues in contact with ILE 458 (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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251C ILE* 4.4 9.7 + - + +
253C PRO* 3.9 13.0 - - + +
393C PHE* 3.7 35.7 - - + +
396C ILE* 3.8 16.6 - - + -
397C ALA* 3.6 44.2 - - + +
418C LEU* 4.1 16.8 - - + -
454C LEU 3.0 16.0 + - - +
455C TYR* 3.7 20.2 - - + +
457C TYR* 1.3 79.2 - - - +
459C SER* 1.3 64.4 + - - +
460C LYS 3.5 0.2 + - - -
461C TYR 3.9 9.5 - - - +
462C THR* 3.7 14.4 - - - +
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Residues in contact with SER 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C PRO* 3.9 18.5 - - - +
455C TYR* 2.5 38.3 + - - -
456C LYS* 3.2 9.5 + - - -
458C ILE* 1.3 81.9 - - - +
460C LYS* 1.3 57.8 + - - +
462C THR* 3.2 15.3 - - - +
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Residues in contact with LYS 460 (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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173A LYS* 5.9 0.4 - - - +
475A LEU 4.6 1.1 + - - -
476A GLN* 2.5 40.4 + - - +
477A CYS 3.6 16.1 + - - -
478A SER* 4.0 13.2 - - - +
456C LYS* 3.4 18.8 + - + +
457C TYR* 3.1 3.1 + - - +
459C SER* 1.3 81.5 + - - +
461C TYR* 1.3 86.7 + - + +
462C THR* 3.1 11.7 + - - +
465C PHE* 3.7 24.6 - - + +
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Residues in contact with TYR 461 (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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476A GLN 5.1 1.9 + - - -
478A SER* 3.5 20.3 + - - -
248C PRO* 5.6 9.9 - - + +
249C ILE 4.7 0.6 - - - +
250C GLY* 3.5 15.3 - - - -
251C ILE 4.4 0.2 + - - -
393C PHE* 4.4 8.0 - - - -
457C TYR* 2.8 70.3 + + + +
458C ILE 3.9 7.7 - - - +
460C LYS* 1.3 93.3 + - + +
462C THR* 1.3 63.2 + - - +
465C PHE* 3.9 39.7 - + + -
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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