Contacts of the helix formed by residues 516 - 533 (chain D) in PDB entry 3HN3
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 LEU 516 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B LYS 4.0 4.0 - - - +
195B TYR* 3.6 24.7 - - + -
196B PRO* 3.4 33.4 - - + -
199B TYR* 3.5 33.4 - - + +
505D TYR* 5.4 0.2 - - - -
506D SER* 5.9 1.8 - - - +
510D ASP* 3.7 13.2 - - + +
513D HIS* 3.6 25.1 - - + +
514D LEU 3.1 1.4 - - - -
515D GLU* 1.3 87.8 - - + +
517D ILE* 1.3 64.1 + - - +
518D GLN 3.4 1.8 - - - -
519D LEU* 3.5 7.3 + - + +
520D GLN* 3.1 37.9 + - - +
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Residues in contact with ILE 517 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D TYR* 3.7 28.3 - - + +
506D SER* 3.7 24.2 - - - +
514D LEU* 3.3 28.0 + - + +
515D GLU 3.5 0.4 - - - -
516D LEU* 1.3 79.1 - - - +
518D GLN* 1.3 64.9 + - - +
520D GLN* 3.9 0.9 - - - +
521D LEU* 3.0 26.5 + - + +
565D LEU* 3.9 19.3 - - + -
568D GLN* 3.6 29.2 - - + +
569D TYR* 3.6 31.9 - - + +
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Residues in contact with GLN 518 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515D GLU 5.0 2.7 + - - +
516D LEU 3.4 0.4 - - - -
517D ILE* 1.3 80.5 - - - +
519D LEU* 1.3 64.5 + - - +
521D LEU* 3.9 4.3 - - - +
522D ALA* 3.0 25.6 + - - +
568D GLN* 2.9 43.6 + - - +
571D LEU* 3.4 37.3 - - + +
572D GLY* 4.3 7.5 - - - +
575D GLN* 5.6 3.5 - - - +
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Residues in contact with LEU 519 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B THR 3.8 15.7 - - - +
193B SER* 3.9 10.1 - - - +
194B LYS 3.5 4.3 - - - +
195B TYR* 3.5 43.1 - - - +
196B PRO* 3.9 9.9 - - + -
515D GLU 5.4 2.6 + - - +
516D LEU* 3.5 11.1 + - + +
517D ILE 3.3 0.2 - - - -
518D GLN* 1.3 79.9 - - - +
520D GLN* 1.3 61.8 + - - +
522D ALA* 3.4 6.5 + - + +
523D THR* 3.0 28.9 + - - +
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Residues in contact with GLN 520 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B SER 4.4 5.4 - - - -
194B LYS* 3.0 53.8 + - - +
195B TYR* 4.1 4.8 - - - -
505D TYR* 3.1 48.7 + - + +
506D SER 4.7 0.9 + - - -
509D HIS* 4.8 0.7 + - - -
510D ASP* 3.2 25.6 + - - +
516D LEU* 3.1 31.0 + - - +
517D ILE 4.1 0.2 - - - +
519D LEU* 1.3 75.1 - - - +
521D LEU* 1.3 56.9 + - - +
523D THR* 3.5 3.4 + - - +
524D GLN* 2.9 27.7 + - - +
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Residues in contact with LEU 521 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D TYR* 3.9 7.1 - - + -
517D ILE* 3.0 19.2 + - + +
518D GLN* 3.9 3.4 - - - +
520D GLN* 1.3 75.3 - - - +
522D ALA* 1.3 65.3 + - - +
524D GLN* 3.3 19.8 - - - +
525D PHE* 3.1 44.4 + - + -
538D GLN* 3.6 18.6 - - - +
568D GLN 4.4 2.0 - - - +
569D TYR* 3.5 66.4 - - + +
572D GLY* 4.0 13.7 - - - -
573D LEU* 4.3 3.8 - - + +
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Residues in contact with ALA 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D GLN 3.0 19.0 + - - +
519D LEU* 3.4 8.3 + - + +
521D LEU* 1.3 73.8 - - - +
523D THR* 1.3 63.7 + - - +
525D PHE* 3.4 4.6 + - - -
526D GLU* 2.8 46.6 + - + +
572D GLY* 5.9 1.5 - - - -
576D LYS* 6.4 0.2 - - - -
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Residues in contact with THR 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B SER* 2.6 50.3 + - - +
194B LYS* 5.4 8.1 - - + +
519D LEU* 3.0 14.4 + - - +
520D GLN* 3.6 4.9 - - - +
522D ALA* 1.3 76.8 - - - +
524D GLN* 1.3 63.2 + - - +
526D GLU* 3.4 5.3 + - - -
527D ASN* 2.8 54.3 + - - +
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Residues in contact with GLN 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D MRD 3.2 21.7 - - + +
501D LEU* 3.8 10.8 - - + +
503D SER* 2.8 20.9 + - - -
505D TYR* 2.7 27.1 + - - +
520D GLN 2.9 15.1 + - - +
521D LEU* 3.3 14.0 - - - +
523D THR* 1.3 76.5 - - - +
525D PHE* 1.3 74.5 + - - +
527D ASN* 3.8 3.0 - - - +
528D TRP* 3.0 44.1 + - + -
538D GLN* 2.7 28.9 + - - +
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Residues in contact with PHE 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501D LEU* 4.8 0.4 - - + -
521D LEU* 3.1 36.1 + - + +
522D ALA* 3.9 5.2 - - - +
524D GLN* 1.3 96.1 - - + +
526D GLU* 1.3 67.3 + - - +
528D TRP* 4.0 0.3 - - - +
529D TYR* 2.9 22.9 + - - +
536D ILE* 3.9 26.1 - - + +
538D GLN* 3.6 18.8 - - + -
572D GLY 4.4 12.8 - - - -
573D LEU* 3.7 26.2 - - + -
576D LYS* 4.3 15.0 - - + -
580D TYR* 3.4 23.3 + - + +
581D VAL* 3.6 26.7 - - + -
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Residues in contact with GLU 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522D ALA* 2.8 45.7 + - + +
523D THR* 4.0 5.2 - - - +
525D PHE* 1.3 77.7 - - - +
527D ASN* 1.3 66.5 + - - +
529D TYR* 5.1 0.4 - - - -
530D LYS* 3.0 29.3 + - - +
576D LYS* 3.5 35.4 + - - +
580D TYR* 3.9 5.8 + - - -
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Residues in contact with ASN 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D TYR* 3.5 58.2 + - + -
523D THR* 2.8 48.1 + - - +
524D GLN* 3.8 4.1 - - - +
526D GLU* 1.3 74.5 - - - +
528D TRP* 1.3 62.7 + - + +
530D LYS* 3.9 6.0 - - - +
531D LYS* 3.3 16.5 + - - +
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Residues in contact with TRP 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D MRD 3.4 18.4 + - + -
483D SER* 4.5 2.2 - - - -
485D SER 3.3 22.4 - - - -
487D TYR* 3.4 33.8 - + + +
490D ASP* 3.4 25.6 - - + -
493D ALA* 3.8 24.2 - - + -
499D ILE* 3.8 21.9 - - + +
501D LEU* 3.4 36.7 - - + +
524D GLN* 3.0 34.0 + - + +
527D ASN* 1.3 78.4 - - + +
529D TYR* 1.3 58.4 + - - +
531D LYS* 3.3 4.1 + - - +
532D TYR* 3.1 51.8 + + - +
536D ILE* 3.9 18.6 - - + -
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Residues in contact with TYR 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D LYS* 2.8 30.6 + - - +
334D SER* 3.8 9.0 - - - -
499D ILE* 5.8 0.2 - - - -
525D PHE 2.9 17.2 + - - +
526D GLU* 4.4 0.9 - - - +
528D TRP* 1.3 75.9 - - - +
530D LYS* 1.3 64.3 + - - +
532D TYR* 5.4 0.2 - - - -
533D GLN* 2.9 42.3 + - + +
534D LYS 3.3 34.3 - - - -
536D ILE* 4.1 3.6 - - + +
580D TYR* 3.4 57.9 - + + +
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Residues in contact with LYS 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526D GLU 3.0 21.2 + - - +
527D ASN* 3.9 6.7 - - - +
529D TYR* 1.3 79.3 - - - +
531D LYS* 1.3 60.9 + - - +
533D GLN* 4.3 14.2 + - - +
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Residues in contact with LYS 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D TYR* 3.7 38.1 - - + +
488D ALA* 4.5 14.7 + - - +
527D ASN 3.3 13.9 + - - +
528D TRP 3.3 5.2 + - - +
529D TYR 3.2 0.4 - - - -
530D LYS* 1.3 81.5 - - - +
532D TYR* 1.3 86.9 + - + +
533D GLN* 5.0 1.6 + - - +
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Residues in contact with TYR 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D TYR 4.1 6.0 + - - -
490D ASP 3.5 11.4 + - - -
493D ALA* 3.4 29.1 - - + +
494D PRO* 3.5 36.7 - - + +
499D ILE* 3.5 25.8 - - + -
528D TRP* 3.1 34.4 + + - +
531D LYS* 1.3 116.9 + - + +
533D GLN* 1.3 72.6 + - - +
534D LYS* 3.2 20.2 + - - +
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Residues in contact with GLN 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D LYS* 3.5 47.2 + - + +
529D TYR* 2.9 44.3 + - + +
530D LYS* 4.3 12.8 + - - +
531D LYS 5.0 1.5 + - - +
532D TYR* 1.3 74.2 - - - +
534D LYS* 1.3 59.7 + - - +
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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
------------------------------------------------------------
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