Contacts of the helix formed by residues 443 - 461 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441A SER 3.6 3.2 + - - -
442A MET* 1.3 78.8 - - - +
444A ASP* 1.3 65.6 + - - +
445A GLU* 3.1 23.4 - - - +
446A GLN* 3.1 26.2 + - - +
447A ARG* 3.0 21.8 + - - +
449A ARG* 5.0 0.9 + - - -
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Residues in contact with ASP 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A LYS* 5.6 0.5 - - - +
442A MET 4.3 3.3 - - - +
443A SER* 1.3 77.7 - - - +
445A GLU* 1.3 70.8 + - - +
447A ARG* 3.8 13.9 + - - +
448A ALA* 3.0 25.1 + - - +
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Residues in contact with GLU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A SER* 3.1 29.2 - - - +
444A ASP* 1.3 85.6 + - - +
446A GLN* 1.3 60.1 - - - +
448A ALA* 3.2 6.5 + - - +
449A ARG* 3.0 36.0 + - - +
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Residues in contact with GLN 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A GLU* 5.3 5.2 + - - +
442A MET* 3.6 26.5 - - + +
443A SER* 3.1 19.4 + - - +
445A GLU* 1.3 77.0 - - - +
447A ARG* 1.3 62.7 + - - +
449A ARG* 3.3 29.7 + - + +
450A LYS* 3.0 49.8 + - + +
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Residues in contact with ARG 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A LYS* 4.3 21.8 - - - +
377A ASP* 4.2 16.7 + - - +
402A ARG* 3.0 34.3 + - - +
403A LYS* 3.0 27.8 + - + +
404A GLY* 3.7 14.2 - - - +
405A VAL* 3.8 11.0 - - + -
439A ALA 4.7 7.0 + - - -
440A VAL 5.7 0.4 + - - -
442A MET* 3.7 43.7 + - + -
443A SER 3.0 15.4 + - - +
444A ASP* 3.8 12.9 + - - +
446A GLN* 1.3 77.5 - - - +
448A ALA* 1.3 57.7 + - - +
450A LYS* 3.3 3.3 + - - +
451A PHE* 2.9 30.8 + - - +
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A LYS* 3.9 30.9 + - + +
444A ASP 3.0 18.8 + - - +
445A GLU* 3.2 6.0 + - - +
447A ARG* 1.3 76.3 - - - +
449A ARG* 1.3 62.3 + - - +
451A PHE* 3.4 3.5 + - - +
452A GLU* 3.1 25.8 + - - +
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Residues in contact with ARG 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A SER* 5.0 1.0 + - - -
445A GLU* 3.0 19.3 + - - +
446A GLN* 3.3 46.2 + - + +
448A ALA* 1.3 78.5 - - - +
450A LYS* 1.3 65.9 + - + +
452A GLU* 3.4 10.2 + - - +
453A LYS* 3.4 30.7 + - - +
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Residues in contact with LYS 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A VAL* 5.8 3.1 - - + -
420A GLY* 3.3 35.2 + - - +
421A SER 5.3 1.4 + - - -
422A LEU* 4.0 23.5 - - + +
438A GLU* 5.2 1.3 - - - -
442A MET* 4.0 21.3 - - + -
446A GLN* 3.0 43.4 + - + +
447A ARG* 3.8 3.6 - - - +
449A ARG* 1.3 82.2 - - + +
451A PHE* 1.3 64.3 + - - +
452A GLU 3.3 0.2 + - - -
453A LYS* 3.3 14.6 + - - +
454A LEU* 3.2 27.7 + - + +
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Residues in contact with PHE 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ILE* 3.4 35.2 - - + -
399A GLN* 3.4 22.7 - - + -
400A GLN* 3.5 32.1 - - + -
403A LYS* 3.8 40.4 - - + -
404A GLY 5.1 4.9 - - - +
447A ARG 2.9 17.4 + - - +
448A ALA 3.8 3.6 - - - +
449A ARG 3.3 0.2 - - - -
450A LYS* 1.3 77.4 - - - +
452A GLU* 1.3 63.3 + - - +
454A LEU* 3.2 10.3 + - + +
455A TYR* 2.8 61.1 + + + -
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Residues in contact with GLU 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A LYS* 4.4 8.1 + - - -
448A ALA 3.1 16.2 + - - +
449A ARG* 3.8 6.1 - - - +
450A LYS 3.2 0.2 - - - -
451A PHE* 1.3 90.3 - - - +
453A LYS* 1.3 66.9 + - + +
455A TYR* 4.4 12.6 - - - +
456A LYS* 2.9 38.7 + - - +
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Residues in contact with LYS 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ASN* 3.6 39.3 + - - +
420A GLY* 4.7 7.7 - - - -
449A ARG* 3.6 28.1 - - - +
450A LYS* 3.3 11.4 + - - +
452A GLU* 1.3 78.2 - - + +
454A LEU* 1.3 62.2 + - - +
456A LYS* 3.4 22.2 + - - +
457A TYR* 3.3 19.6 + - - +
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Residues in contact with LEU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ILE* 3.8 33.2 - - + -
404A GLY 5.7 3.6 - - - +
406A LEU* 4.4 15.7 - - + +
418A LEU* 3.3 36.3 - - + +
419A ASN 3.2 22.4 - - - +
420A GLY 3.9 14.6 - - - +
421A SER* 3.8 5.6 - - - +
450A LYS* 3.2 18.9 + - + +
451A PHE* 3.5 11.2 - - + +
453A LYS* 1.3 78.1 - - - +
455A TYR* 1.3 65.4 + - - +
457A TYR* 3.1 14.4 + - - +
458A ILE* 3.1 18.2 + - - +
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Residues in contact with TYR 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A PRO* 4.7 8.3 - - + +
257A THR* 3.6 23.7 - - - +
396A ILE* 3.8 11.2 - - + -
397A ALA* 4.0 14.4 - - + -
400A GLN* 3.7 30.8 + - + -
451A PHE* 2.8 46.8 + + + +
452A GLU* 4.1 13.7 - - - +
454A LEU* 1.3 73.5 - - - +
456A LYS* 1.3 54.5 + - - +
458A ILE* 3.4 24.9 + - + +
459A SER* 2.5 50.1 + - - -
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Residues in contact with LYS 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A GLU* 2.9 29.9 + - - +
453A LYS* 3.5 21.6 - - - +
455A TYR* 1.3 78.3 - - - +
457A TYR* 1.3 62.1 + - - +
459A SER* 3.1 14.0 + - - -
460A LYS* 3.4 13.0 + - - +
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Residues in contact with TYR 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A PRO* 4.2 18.2 + - - +
249A ILE 5.0 2.0 + - - -
388A MET* 6.1 0.2 - - - -
393A PHE* 3.6 27.6 - + - -
417A SER* 3.2 47.7 + - - +
418A LEU* 3.8 16.6 - - + -
419A ASN 6.0 0.4 - - - +
453A LYS 3.3 8.7 + - - +
454A LEU* 3.1 10.3 + - - +
456A LYS* 1.3 79.8 - - - +
458A ILE* 1.3 63.2 + - - +
460A LYS* 3.1 2.0 + - - -
461A TYR* 2.9 74.3 + + + +
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Residues in contact with ILE 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ILE* 4.3 5.8 - - + +
253A PRO* 3.8 16.9 - - + +
393A PHE* 3.7 35.4 - - + +
396A ILE* 3.8 16.6 - - + -
397A ALA* 3.7 41.7 - - + +
418A LEU* 4.1 15.5 - - + -
454A LEU 3.1 10.9 + - - +
455A TYR* 3.4 24.7 - - + +
457A TYR* 1.3 80.7 - - - +
459A SER* 1.3 65.4 + - - +
461A TYR 4.0 6.9 - - - +
462A THR* 3.6 15.9 - - - +
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Residues in contact with SER 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PRO* 3.9 16.2 - - - +
455A TYR* 2.5 41.1 + - - -
456A LYS* 3.1 14.2 + - - -
458A ILE* 1.3 79.8 - - - +
460A LYS* 1.3 58.4 + - - +
462A THR* 3.6 10.7 - - - +
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Residues in contact with LYS 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A LYS 3.4 10.3 + - - +
457A TYR 3.1 6.3 + - - +
459A SER* 1.3 82.7 + - - +
461A TYR* 1.3 106.8 + - + +
462A THR* 3.1 9.9 + - - +
465A PHE* 3.9 27.7 - - + +
173C LYS* 5.1 6.9 - - - +
475C LEU 4.1 15.0 + - - -
476C GLN* 5.7 0.2 - - - +
477C CYS 4.7 3.4 + - - -
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Residues in contact with TYR 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A PRO* 5.5 10.3 - - + +
249A ILE 4.6 1.4 - - - +
250A GLY* 3.5 17.5 - - - -
251A ILE 4.4 0.2 + - - -
393A PHE* 4.3 7.6 - - - -
457A TYR* 2.9 68.9 + + + +
458A ILE 4.0 6.6 - - - +
460A LYS* 1.3 115.8 + - + +
462A THR* 1.3 62.2 + - - +
465A PHE* 4.0 33.2 - + + -
475C LEU 4.8 0.9 + - - -
476C GLN* 4.7 16.6 + - - -
477C CYS 4.2 10.9 + - - -
478C SER* 5.4 2.3 - - - -
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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