Contacts of the helix formed by residues 516 - 533 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LYS 3.7 11.0 - - - +
195A TYR* 3.7 17.5 - - + -
196A PRO* 3.4 33.2 - - + -
199A TYR* 3.7 18.2 - - + +
505E TYR* 5.9 0.4 - - + -
506E SER* 5.9 1.6 - - - +
510E ASP* 3.7 22.4 - - + -
513E HIS* 3.1 33.7 + - + +
515E GLU* 1.3 85.4 - - + +
517E ILE* 1.3 64.1 + - + +
518E GLN 3.5 1.8 - - - -
519E LEU* 3.4 8.4 + - + +
520E GLN* 3.0 38.2 + - - +
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Residues in contact with ILE 517 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505E TYR* 3.7 30.8 - - + +
506E SER* 3.7 21.1 - - - +
514E LEU* 3.4 34.1 + - + +
515E GLU 3.5 0.2 - - - -
516E LEU* 1.3 75.7 - - - +
518E GLN* 1.3 66.3 + - - +
520E GLN* 3.3 1.2 + - - +
521E LEU* 2.9 27.0 + - + +
565E LEU* 4.0 14.6 - - + -
568E GLN* 3.8 30.5 - - + +
569E TYR* 3.5 30.1 - - + -
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Residues in contact with GLN 518 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514E LEU 4.9 0.2 + - - -
515E GLU 5.0 3.4 + - - +
516E LEU 3.5 0.4 - - - -
517E ILE* 1.3 79.3 - - - +
519E LEU* 1.3 57.3 + - - +
521E LEU* 3.8 4.7 - - - +
522E ALA* 2.9 30.7 + - - +
568E GLN* 2.9 43.6 + - - +
571E LEU* 3.4 36.7 - - + +
572E GLY* 4.4 10.1 - - - +
575E GLN* 5.7 2.9 - - - +
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Residues in contact with LEU 519 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A THR 3.8 17.5 - - - +
193A SER* 3.8 11.2 - - - +
194A LYS 3.5 4.9 - - - +
195A TYR* 3.4 42.0 - - - +
196A PRO* 3.9 9.9 - - + -
515E GLU 5.3 3.0 + - - +
516E LEU* 3.4 11.1 + - + +
517E ILE 3.2 0.6 - - - -
518E GLN* 1.3 77.7 - - - +
520E GLN* 1.3 64.8 + - - +
522E ALA* 3.3 8.5 + - + +
523E THR* 3.1 28.9 + - - +
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Residues in contact with GLN 520 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A SER 4.3 5.2 - - - -
194A LYS* 3.0 53.9 + - + +
195A TYR* 4.2 3.4 - - - -
505E TYR* 3.1 49.1 + - + +
506E SER 4.9 0.7 + - - -
509E HIS* 4.9 0.9 + - - -
510E ASP* 3.3 26.7 + - - +
516E LEU* 3.0 30.0 + - - +
519E LEU* 1.3 78.6 - - - +
521E LEU* 1.3 58.2 + - - +
523E THR* 3.5 3.4 + - - +
524E GLN* 2.9 27.2 + - - +
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Residues in contact with LEU 521 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505E TYR* 3.7 7.7 - - + -
517E ILE* 2.9 19.0 + - + +
518E GLN* 3.8 3.4 - - - +
520E GLN* 1.3 75.7 - - - +
522E ALA* 1.3 64.0 + - - +
524E GLN* 3.3 34.8 + - - +
525E PHE* 3.1 46.2 + - + -
538E GLN* 3.7 10.8 - - - +
568E GLN 4.9 0.4 - - - +
569E TYR* 3.7 56.5 - - + +
572E GLY* 3.9 16.8 - - - -
573E LEU* 4.1 2.7 - - + +
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Residues in contact with ALA 522 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518E GLN 2.9 18.9 + - - +
519E LEU* 3.6 9.2 - - + +
521E LEU* 1.3 75.5 - - - +
523E THR* 1.3 63.8 + - - +
525E PHE* 3.4 6.3 + - - +
526E GLU* 3.0 31.6 + - - +
572E GLY* 5.9 1.4 - - - -
576E LYS* 6.0 1.7 - - - -
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Residues in contact with THR 523 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A SER* 2.6 50.2 + - - +
194A LYS* 5.5 2.9 - - + -
519E LEU* 3.1 14.3 + - - +
520E GLN* 3.6 5.8 - - - +
522E ALA* 1.3 77.1 - - - +
524E GLN* 1.3 56.0 + - - +
526E GLU* 3.8 5.5 - - - +
527E ASN* 2.9 57.0 + - - +
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Residues in contact with GLN 524 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E MPD 3.1 26.1 - - + +
501E LEU* 3.8 8.8 - - + +
503E SER* 2.9 18.4 + - - -
505E TYR* 2.6 26.4 + - - +
520E GLN 2.9 15.0 + - - +
521E LEU* 3.4 14.4 - - - +
523E THR* 1.3 78.1 - - - +
525E PHE* 1.3 75.6 + - - +
527E ASN* 3.9 3.0 - - - +
528E TRP* 3.0 46.8 + - + +
538E GLN* 2.9 27.1 + - - -
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Residues in contact with PHE 525 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501E LEU* 4.9 0.9 - - + -
521E LEU* 3.1 41.3 + - + +
522E ALA* 4.0 5.2 - - - +
524E GLN* 1.3 94.7 - - + +
526E GLU* 1.3 67.1 + - - +
528E TRP* 4.0 2.8 - - - +
529E TYR* 3.0 21.8 + - - +
536E ILE* 4.1 22.8 - - + +
538E GLN* 3.6 20.0 - - + -
572E GLY 4.3 11.4 - - - -
573E LEU* 3.8 24.0 - - + -
576E LYS* 4.2 17.7 - - + -
580E TYR* 3.2 24.8 + - + +
581E VAL* 3.7 26.2 - - + -
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Residues in contact with GLU 526 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522E ALA* 3.0 21.0 + - - +
523E THR* 3.8 5.8 - - - +
525E PHE* 1.3 77.8 - - - +
527E ASN* 1.3 65.7 + - - +
529E TYR* 4.4 0.6 - - - +
530E LYS* 3.1 29.8 + - + +
576E LYS* 5.6 5.8 - - - +
580E TYR* 3.7 6.9 + - - +
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Residues in contact with ASN 527 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487E TYR* 3.6 49.3 + - + -
523E THR* 2.9 41.8 + - - +
524E GLN* 3.9 4.6 - - - +
526E GLU* 1.3 79.1 - - - +
528E TRP* 1.3 66.5 + - + +
530E LYS* 3.9 6.0 - - - +
531E LYS* 3.2 24.3 + - - +
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Residues in contact with TRP 528 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E MPD 3.2 18.5 + - + -
483E SER* 4.4 1.8 - - - -
485E SER 3.3 21.8 - - - -
487E TYR* 3.4 27.0 - + + +
490E ASP* 3.5 31.2 - - + -
493E ALA* 3.9 24.0 - - + -
499E ILE* 3.8 19.3 - - + -
501E LEU* 3.3 40.3 - - + +
524E GLN* 3.0 33.9 + - + +
527E ASN* 1.3 77.5 - - + +
529E TYR* 1.3 59.0 + - - +
531E LYS* 3.3 2.9 + - - -
532E TYR* 3.0 55.7 + + - +
536E ILE* 3.8 18.6 - - + -
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Residues in contact with TYR 529 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E LYS* 2.6 35.3 + - - +
334E SER* 3.9 8.1 - - - -
499E ILE* 6.0 0.2 - - - -
525E PHE 3.0 17.5 + - - +
526E GLU 4.4 1.1 - - - +
528E TRP* 1.3 74.8 - - - +
530E LYS* 1.3 67.9 + - - +
533E GLN* 2.9 36.9 + - + +
534E LYS 3.3 36.6 - - - -
536E ILE* 4.1 3.7 - - + +
580E TYR* 3.4 54.3 - + + +
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Residues in contact with LYS 530 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526E GLU* 3.1 22.8 + - + +
527E ASN* 3.9 6.3 - - - +
528E TRP 3.4 0.2 - - - -
529E TYR* 1.3 79.5 - - - +
531E LYS* 1.3 61.9 + - - +
533E GLN* 4.0 11.3 - - - +
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Residues in contact with LYS 531 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487E TYR* 3.6 38.8 + - + +
488E ALA* 4.1 18.5 + - - +
490E ASP 5.1 0.2 + - - -
527E ASN 3.2 14.7 + - - +
529E TYR 3.2 0.4 - - - -
530E LYS* 1.3 82.5 - - - +
532E TYR* 1.3 103.8 + - + +
533E GLN* 4.0 7.6 + - - -
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Residues in contact with TYR 532 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487E TYR 3.8 10.8 + - - -
490E ASP 3.3 19.4 + - - -
493E ALA* 3.4 24.9 - - + +
494E PRO* 3.7 32.2 - - + +
499E ILE* 3.4 25.8 - - + -
528E TRP* 3.0 30.0 + + - +
531E LYS* 1.3 124.9 + - + +
533E GLN* 1.3 80.0 + - - +
534E LYS* 3.3 15.9 + - - +
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Residues in contact with GLN 533 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E LYS* 3.5 41.5 + - + +
529E TYR* 2.9 45.6 + - + +
530E LYS* 4.0 11.0 - - - +
531E LYS 4.0 8.1 + - - -
532E TYR* 1.3 86.0 + - - +
534E LYS* 1.3 60.6 + - - +
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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