Contacts of the helix formed by residues 443 - 461 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441B SER 3.6 2.8 + - - -
442B MET* 1.3 79.1 - - - +
444B ASP* 1.3 66.4 + - - +
445B GLU* 3.5 19.1 - - - +
446B GLN* 3.3 25.9 + - - +
447B ARG* 3.0 21.5 + - - +
449B ARG* 5.4 0.2 + - - -
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Residues in contact with ASP 444 (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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403B LYS* 5.8 0.3 - - - +
442B MET 5.0 1.5 - - - +
443B SER* 1.3 75.9 - - - +
445B GLU* 1.3 67.9 + - - +
447B ARG* 3.6 16.1 + - - +
448B ALA* 2.9 30.7 + - - +
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Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B SER* 3.5 20.2 - - - +
444B ASP* 1.3 88.7 + - - +
446B GLN* 1.3 51.5 - - - +
448B ALA* 3.1 7.1 + - - +
449B ARG* 2.7 46.5 + - + +
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Residues in contact with GLN 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B GLU* 5.4 4.9 + - - +
442B MET* 3.5 22.9 - - + +
443B SER* 3.3 18.2 + - - +
445B GLU* 1.3 76.9 - - - +
447B ARG* 1.3 58.6 + - - +
449B ARG* 3.2 36.2 + - - +
450B LYS* 2.9 63.6 + - - +
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Residues in contact with ARG 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LYS* 4.2 22.2 - - - +
377B ASP* 4.1 18.3 + - - +
402B ARG* 3.1 35.3 + - - +
403B LYS* 3.1 21.0 + - + +
404B GLY* 3.6 14.9 - - - +
405B VAL* 3.9 11.9 - - + +
439B ALA 4.6 6.7 + - - -
440B VAL 6.0 0.2 - - - -
442B MET* 3.4 44.8 + - + -
443B SER 3.0 17.0 + - - +
444B ASP* 3.6 14.3 + - - +
446B GLN* 1.3 78.4 - - - +
448B ALA* 1.3 56.9 + - - +
450B LYS* 3.4 2.5 + - - +
451B PHE* 2.8 32.8 + - - +
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Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B LYS* 4.2 26.7 - - + +
444B ASP 2.9 19.0 + - - +
445B GLU* 3.5 6.5 - - - +
447B ARG* 1.3 72.5 - - - +
449B ARG* 1.3 66.2 + - - +
451B PHE* 3.5 3.0 + - - +
452B GLU* 3.1 27.4 + - - +
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Residues in contact with ARG 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B GLU* 2.7 23.2 + - - +
446B GLN* 3.4 50.3 - - - +
448B ALA* 1.3 72.5 - - - +
450B LYS* 1.3 67.2 + - + +
452B GLU* 3.2 15.3 + - - +
453B LYS* 3.4 26.6 + - - +
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Residues in contact with LYS 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B VAL* 5.6 3.1 - - + -
420B GLY* 3.2 35.7 + - - +
421B SER 5.5 1.0 + - - -
422B LEU* 4.2 17.0 - - + +
438B GLU* 5.3 1.3 + - - -
442B MET* 3.9 28.9 - - + -
446B GLN* 2.9 48.0 + - + +
447B ARG* 3.9 3.6 - - - +
449B ARG* 1.3 77.1 - - + +
451B PHE* 1.3 63.6 + - - +
452B GLU 3.2 0.5 + - - -
453B LYS* 3.3 15.5 + - - +
454B LEU* 3.2 27.5 + - + +
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Residues in contact with PHE 451 (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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396B ILE* 3.4 34.5 - - + -
399B GLN* 3.4 22.2 - - + -
400B GLN* 3.4 45.1 - - + -
403B LYS* 3.7 37.5 - - + -
404B GLY 5.0 6.1 - - - +
447B ARG 2.8 19.0 + - - +
448B ALA 3.8 3.1 - - - +
450B LYS* 1.3 77.3 - - - +
452B GLU* 1.3 64.8 + - - +
454B LEU* 3.2 9.5 + - + +
455B TYR* 2.7 52.5 + + + -
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Residues in contact with GLU 452 (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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400B GLN* 5.8 1.6 + - - -
403B LYS* 4.5 7.4 + - - -
448B ALA* 3.1 14.5 + - - +
449B ARG* 3.5 11.4 - - - +
450B LYS 3.2 0.2 - - - -
451B PHE* 1.3 88.9 - - - +
453B LYS* 1.3 68.0 + - + +
455B TYR* 4.7 11.0 - - - +
456B LYS* 3.0 33.6 + - + +
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Residues in contact with LYS 453 (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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419B ASN* 3.6 47.4 + - + +
420B GLY* 4.5 8.3 - - - -
449B ARG* 3.7 25.4 - - - +
450B LYS* 3.3 13.9 + - - +
452B GLU* 1.3 77.0 - - + +
454B LEU* 1.3 62.1 + - - +
456B LYS* 3.6 17.7 - - - +
457B TYR* 3.1 20.8 + - - +
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Residues in contact with LEU 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ILE* 3.7 33.2 - - + -
406B LEU* 4.4 11.9 - - + +
418B LEU* 3.5 35.7 - - + +
419B ASN 3.3 20.9 - - - +
420B GLY 3.8 16.6 - - - +
421B SER* 3.9 8.5 - - - +
450B LYS* 3.2 18.8 + - + +
451B PHE* 3.5 9.4 - - + +
452B GLU 3.2 0.4 - - - -
453B LYS* 1.3 76.0 - - - +
455B TYR* 1.3 65.4 - - - +
457B TYR* 3.0 15.7 + - - +
458B ILE* 3.0 18.2 + - - +
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Residues in contact with TYR 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PRO* 4.9 8.1 - - + +
257B THR* 3.6 17.7 - - - +
396B ILE* 3.7 25.4 - - + -
397B ALA* 4.0 15.7 - - + -
400B GLN* 3.5 40.2 + - + -
451B PHE* 2.7 48.4 + + + +
452B GLU* 4.1 10.1 - - - +
454B LEU* 1.3 74.5 - - - +
456B LYS* 1.3 54.0 + - - +
458B ILE* 3.6 8.7 - - + +
459B SER* 2.4 51.6 + - - -
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Residues in contact with LYS 456 (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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452B GLU* 3.0 25.5 + - + +
453B LYS* 3.6 14.2 - - - +
455B TYR* 1.3 79.0 - - - +
457B TYR* 1.3 65.1 + - - +
459B SER* 3.1 14.3 + - - -
460B LYS* 3.2 14.5 + - + +
478D SER* 5.6 10.1 - - - +
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Residues in contact with TYR 457 (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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248B PRO* 4.4 17.7 + - - +
249B ILE 5.3 1.7 + - - -
393B PHE* 3.8 21.9 - + - -
417B SER* 3.3 50.9 + - - +
418B LEU* 4.0 15.0 - - + -
453B LYS 3.1 9.3 + - - +
454B LEU* 3.0 11.4 + - - +
456B LYS* 1.3 79.8 - - - +
458B ILE* 1.3 64.5 + - + +
460B LYS 3.1 2.6 + - - -
461B TYR* 3.0 77.5 + + + +
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Residues in contact with ILE 458 (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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251B ILE* 4.3 10.8 - - + +
253B PRO* 3.8 11.4 - - + +
393B PHE* 3.6 38.3 - - + +
396B ILE* 3.7 21.1 - - + -
397B ALA* 3.5 41.5 - - + +
418B LEU* 4.1 17.3 - - + -
454B LEU 3.0 14.3 + - - +
455B TYR* 3.6 17.3 - - + +
457B TYR* 1.3 80.4 - - + +
459B SER* 1.3 65.8 + - - +
460B LYS 3.6 0.2 + - - -
461B TYR 4.1 5.8 - - - +
462B THR* 3.6 16.1 - - - +
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Residues in contact with SER 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PRO* 4.0 15.2 - - - +
455B TYR* 2.4 49.3 + - - -
456B LYS* 3.1 13.0 + - - -
458B ILE* 1.3 78.4 - - - +
460B LYS* 1.3 55.1 + - - +
462B THR* 3.4 13.9 - - - +
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Residues in contact with LYS 460 (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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456B LYS* 3.2 17.3 + - + +
457B TYR 3.1 3.2 + - - +
459B SER* 1.3 78.1 + - - +
461B TYR* 1.3 101.1 + - + +
462B THR* 3.1 12.1 + - - +
465B PHE* 3.8 18.7 - - + +
475D LEU 4.9 0.7 - - - -
476D GLN* 2.2 36.7 + - - +
477D CYS* 2.8 29.7 - - - +
478D SER* 3.0 11.3 - - - +
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Residues in contact with TYR 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PRO* 5.6 8.5 - - + +
249B ILE 4.6 1.7 - - - +
250B GLY* 3.5 14.9 - - - -
393B PHE* 4.4 7.4 - - - -
457B TYR* 3.0 66.6 + + + +
458B ILE 4.1 6.2 - - - +
460B LYS* 1.3 111.2 + - + +
462B THR* 1.3 63.8 + - - +
465B PHE* 3.7 37.7 - + + -
476D GLN 4.2 1.2 + - - -
477D CYS* 5.2 0.3 - - - -
478D SER* 3.4 12.8 + - - -
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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
------------------------------------------------------------
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