Contacts of the helix formed by residues 616 - 632 (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 LYS 616 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545D THR* 2.9 34.2 + - + +
547D ALA* 4.6 15.0 - - + +
559D GLU* 3.7 10.8 - - - +
562D GLN* 3.9 17.9 - - - +
591D ASP* 2.7 40.0 + - - -
605D LYS 2.9 4.9 + - - -
607D GLY 2.8 24.1 + - - +
608D ILE* 3.0 16.9 + - - +
609D PHE 4.0 7.9 - - - -
610D THR* 4.2 15.7 - - + +
614D GLN 3.5 0.4 + - - -
615D PRO* 1.3 77.1 - - - +
617D SER* 1.3 68.3 + - - +
618D ALA 3.3 1.1 - - - +
619D ALA* 3.1 15.2 + - - +
620D PHE* 3.7 5.6 - - - -
550E HIS* 4.1 7.0 - - - -
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Residues in contact with SER 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559D GLU* 2.9 25.3 + - - -
563D LYS* 4.2 22.6 - - - +
616D LYS* 1.3 71.6 - - - +
618D ALA* 1.3 61.4 + - - +
620D PHE* 3.2 28.5 + - - +
621D LEU* 3.7 4.5 + - - +
550E HIS* 3.8 10.4 - - - -
559E GLU* 5.3 0.3 - - - +
560E GLU* 4.7 2.3 + - - -
563E LYS* 5.7 2.9 - - - +
617E SER* 2.7 33.2 + - - -
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Residues in contact with ALA 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559D GLU* 4.8 1.6 + - - +
562D GLN* 3.3 43.3 + - + +
563D LYS* 4.0 18.1 - - + +
566D LEU* 4.0 16.5 - - + +
608D ILE* 4.6 5.4 - - + -
616D LYS* 3.3 1.7 - - + +
617D SER* 1.3 75.5 - - - +
619D ALA* 1.3 65.8 + - - +
621D LEU* 3.1 6.7 + - - +
622D LEU* 3.0 24.3 + - - +
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Residues in contact with ALA 619 (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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375D TRP* 4.4 11.2 - - + -
376D LEU* 3.6 6.5 - - + +
608D ILE* 3.4 36.4 + - + +
609D PHE* 4.5 5.6 - - + -
615D PRO* 3.5 18.8 - - + -
616D LYS 3.1 15.6 + - - +
618D ALA* 1.3 77.5 - - - +
620D PHE* 1.3 57.9 + - - +
622D LEU* 3.5 0.6 + - - +
623D ARG* 2.9 29.3 + - - +
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Residues in contact with PHE 620 (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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375D TRP* 3.5 24.7 - + - -
615D PRO* 3.6 31.9 - - + -
616D LYS 3.7 10.8 - - - -
617D SER* 3.2 12.9 + - - +
618D ALA 3.2 0.8 - - - -
619D ALA* 1.3 74.1 - - - +
621D LEU* 1.3 65.7 + - - +
623D ARG* 3.4 17.2 + - - +
624D GLU* 3.1 29.8 + - + +
552E ASP* 4.2 11.4 - - + -
560E GLU* 3.4 39.5 - - + -
563E LYS* 5.8 10.1 - - + +
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Residues in contact with LEU 621 (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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563D LYS* 3.7 39.5 - - + +
566D LEU* 4.3 7.6 - - + -
567D GLU* 3.6 36.1 - - + +
570D HIS* 3.5 32.8 - - + +
617D SER 3.7 3.5 + - - +
618D ALA* 3.1 14.5 + - - +
620D PHE* 1.3 80.0 - - - +
622D LEU* 1.3 63.4 + - - +
624D GLU* 3.3 9.8 + - - +
625D ARG* 3.2 18.2 + - + +
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Residues in contact with LEU 622 (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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376D LEU* 4.4 4.3 - - + -
541D TYR* 3.5 11.2 - - - +
566D LEU* 4.6 3.8 - - + -
570D HIS* 3.3 32.5 - - + +
586D ILE* 3.6 37.9 - - + -
608D ILE* 3.9 16.6 - - + -
618D ALA 3.0 14.3 + - - +
619D ALA* 3.9 5.4 - - - +
621D LEU* 1.3 75.9 - - - +
623D ARG* 1.3 66.6 + - - +
625D ARG* 3.1 6.2 + - - +
626D TYR* 2.9 59.5 + - + +
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Residues in contact with ARG 623 (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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375D TRP* 3.0 77.9 + - - +
376D LEU* 3.3 18.4 - - + +
619D ALA 2.9 19.6 + - - +
620D PHE* 3.5 16.9 + - - +
621D LEU 3.3 0.2 - - - -
622D LEU* 1.3 76.9 - - - +
624D GLU* 1.3 72.8 + - + +
626D TYR 3.2 0.9 + - - -
627D TRP* 3.0 42.8 + - + +
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Residues in contact with GLU 624 (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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620D PHE* 3.1 17.9 + - + +
621D LEU* 3.4 11.7 - - - +
623D ARG* 1.3 85.6 + - + +
625D ARG* 1.3 58.4 + - - +
627D TRP* 3.6 4.3 + - - +
628D LYS* 3.0 30.8 + - - +
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Residues in contact with ARG 625 (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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570D HIS* 3.3 54.5 + - - +
573D LEU* 3.6 12.1 - - - +
574D ASP* 2.8 35.3 + - - -
577D ARG* 3.8 8.7 - - - +
584D GLU* 2.9 36.9 + - - -
621D LEU* 3.2 9.0 + - + +
622D LEU* 3.1 13.1 + - - +
624D GLU* 1.3 80.2 - - - +
626D TYR* 1.3 61.0 + - + +
628D LYS* 3.2 29.0 + - - +
629D ILE* 2.9 43.6 + - + +
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Residues in contact with TYR 626 (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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346D HIS* 3.6 42.3 - - + +
347D GLY* 2.6 36.3 + - - -
376D LEU* 3.4 36.1 - - + +
377D GLY* 3.5 17.9 - - - +
378D ALA 4.0 2.0 - - - -
541D TYR* 4.7 0.9 + - - -
584D GLU* 3.5 28.6 + - - +
586D ILE* 4.1 5.2 + - - +
622D LEU* 2.9 47.4 + - + +
625D ARG* 1.3 85.4 - - + +
627D TRP* 1.3 57.9 + - - +
629D ILE* 3.4 4.9 + - + +
630D ALA* 2.9 30.7 + - - +
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Residues in contact with TRP 627 (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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291D TYR* 3.4 14.6 - + - -
292D LEU* 3.7 27.4 - - + -
374D ARG 3.4 20.9 - - - -
375D TRP* 2.9 22.3 + - - -
376D LEU 3.8 4.0 - - - -
377D GLY* 3.3 12.3 - - - +
623D ARG* 3.0 44.6 + - + +
624D GLU* 4.1 3.6 - - - +
626D TYR* 1.3 76.1 - - - +
628D LYS* 1.3 58.2 + - - +
630D ALA* 3.8 2.0 - - + +
631D ASN* 2.9 55.0 + - - +
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Residues in contact with LYS 628 (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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574D ASP* 5.2 3.6 + - - -
577D ARG* 4.8 12.3 - - - +
624D GLU 3.0 18.5 + - - +
625D ARG* 3.2 38.7 + - - +
627D TRP* 1.3 76.0 - - - +
629D ILE* 1.3 61.2 + - - +
631D ASN* 3.3 8.7 + - - +
632D GLU* 3.2 28.5 + - + +
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Residues in contact with ILE 629 (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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344D TYR* 4.1 27.1 - - + -
346D HIS* 3.7 26.7 - - + +
577D ARG* 3.8 31.4 - - - +
584D GLU* 4.1 3.8 - - - +
625D ARG* 2.9 60.8 + - + +
626D TYR* 3.9 4.3 - - + +
628D LYS* 1.3 71.8 - - - +
630D ALA* 1.3 66.6 + - - +
632D GLU* 3.1 26.1 + - - +
633D THR 4.2 2.6 + - - +
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Residues in contact with ALA 630 (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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292D LEU* 3.8 45.0 - - + +
346D HIS* 4.0 13.4 + - - +
626D TYR 2.9 18.2 + - - +
627D TRP* 3.8 6.3 - - + +
629D ILE* 1.3 77.2 - - - +
631D ASN* 1.3 65.0 + - - +
633D THR* 3.4 19.9 + - - +
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Residues in contact with ASN 631 (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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292D LEU* 6.1 0.2 - - - +
627D TRP* 2.9 46.7 + - - +
628D LYS* 3.8 7.2 - - - +
629D ILE 3.2 0.4 - - - -
630D ALA* 1.3 74.7 - - - +
632D GLU* 1.3 60.0 + - - +
633D THR* 2.9 16.4 + - - +
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Residues in contact with GLU 632 (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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577D ARG* 2.9 44.2 + - - -
578D ARG* 3.5 24.2 + - - +
628D LYS* 3.2 23.1 + - + +
629D ILE* 3.1 18.1 + - - +
631D ASN* 1.3 71.4 - - - +
633D THR* 1.3 70.8 + - - +
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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
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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