Contacts of the helix formed by residues 616 - 633 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A HIS* 4.0 7.6 - - - +
545B THR* 2.9 35.9 + - + +
547B ALA* 4.5 16.6 - - + +
559B GLU* 4.2 6.3 - - + +
562B GLN* 4.0 18.2 - - - +
591B ASP* 2.7 40.0 + - - -
605B LYS 3.0 5.5 + - - -
607B GLY 2.8 23.7 + - - +
608B ILE 2.9 16.1 + - - +
609B PHE 4.1 7.6 - - - -
610B THR* 4.4 15.3 - - + +
614B GLN 3.6 0.6 + - - -
615B PRO* 1.3 79.3 - - - +
617B SER* 1.3 67.8 + - - +
618B ALA 3.2 0.9 - - - +
619B ALA* 3.1 15.2 + - - +
620B PHE* 3.7 3.2 - - - -
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Residues in contact with SER 617 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A HIS* 3.8 8.5 - - - -
560A GLU* 4.7 2.8 + - - -
563A LYS* 5.4 2.5 - - - +
617A SER* 2.4 35.3 + - - -
559B GLU* 3.1 21.6 + - - -
563B LYS* 4.0 23.6 - - - +
616B LYS* 1.3 75.2 - - - +
618B ALA* 1.3 61.1 + - - +
620B PHE* 3.2 28.2 + - - +
621B LEU* 3.7 3.8 + - - +
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Residues in contact with ALA 618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B GLU* 5.0 1.6 + - - +
562B GLN* 3.3 41.0 + - + +
563B LYS* 3.8 22.0 - - + +
566B LEU* 4.0 15.0 - - + +
608B ILE* 4.7 4.5 - - + -
616B LYS* 3.2 2.0 - - + +
617B SER* 1.3 76.2 - - - +
619B ALA* 1.3 65.2 + - - +
620B PHE 3.1 0.2 - - - -
621B LEU* 3.1 6.5 + - - +
622B LEU* 3.0 23.2 + - - +
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Residues in contact with ALA 619 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B TRP* 4.5 6.3 - - + -
376B LEU* 3.6 6.4 - - - +
608B ILE* 3.5 36.8 + - + +
609B PHE* 4.4 10.5 - - + -
615B PRO* 3.6 18.2 - - + -
616B LYS 3.1 14.7 + - - +
618B ALA* 1.3 77.2 - - - +
620B PHE* 1.3 57.3 + - - +
622B LEU* 3.5 1.4 + - - +
623B ARG* 2.9 29.0 + - - +
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Residues in contact with PHE 620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ASP* 4.4 11.7 - - + -
560A GLU* 3.5 39.5 - - + -
563A LYS* 5.7 14.4 - - + +
375B TRP* 3.6 24.7 - + - -
615B PRO* 3.7 30.1 - - + -
616B LYS 3.7 5.8 - - - -
617B SER* 3.2 17.0 + - - +
618B ALA 3.1 0.6 - - - -
619B ALA* 1.3 74.6 - - - +
621B LEU* 1.3 61.3 + - - +
623B ARG* 3.4 17.6 + - - +
624B GLU* 3.0 36.9 + - + +
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Residues in contact with LEU 621 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B LYS* 4.8 17.0 - - + +
566B LEU* 4.5 8.7 - - + -
567B GLU* 4.4 29.8 - - + +
570B HIS* 3.6 31.2 - - + +
617B SER 3.7 2.5 + - - +
618B ALA* 3.1 17.1 + - + +
620B PHE* 1.3 78.7 - - - +
622B LEU* 1.3 64.0 + - - +
624B GLU* 3.3 12.7 + - + +
625B ARG* 3.2 18.6 + - + +
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Residues in contact with LEU 622 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LEU* 4.3 4.9 - - + -
541B TYR* 3.7 9.0 - - - +
566B LEU* 4.7 5.2 - - + -
570B HIS* 3.6 28.3 - - + +
586B ILE* 3.5 36.8 - - + -
608B ILE* 3.8 17.5 - - + -
618B ALA 3.0 13.7 + - - +
619B ALA* 3.8 5.6 - - - +
621B LEU* 1.3 76.8 - - - +
623B ARG* 1.3 61.0 + - - +
625B ARG* 3.2 5.7 + - - +
626B TYR* 2.9 70.0 + - + +
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Residues in contact with ARG 623 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B TRP* 3.0 77.4 + - - +
376B LEU* 3.4 18.7 - - + +
619B ALA 2.9 17.5 + - - +
620B PHE* 3.6 18.0 + - - +
622B LEU* 1.3 76.7 - - - +
624B GLU* 1.3 76.9 + - - +
626B TYR 3.3 0.7 + - - -
627B TRP* 3.1 40.8 + - + +
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Residues in contact with GLU 624 (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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620B PHE* 3.0 21.3 + - + +
621B LEU* 3.5 14.4 - - + +
622B LEU 3.3 0.2 - - - -
623B ARG* 1.3 96.7 + - - +
625B ARG* 1.3 62.7 + - - +
627B TRP* 3.5 3.5 + - - +
628B LYS* 3.1 25.4 + - - +
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Residues in contact with ARG 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B HIS* 3.3 56.2 + - - +
573B LEU* 3.7 10.9 - - - +
574B ASP* 2.9 32.7 + - - -
577B ARG* 3.7 7.9 - - - +
584B GLU* 2.8 40.8 + - - -
621B LEU* 3.2 9.4 + - + +
622B LEU* 3.2 13.3 + - - +
624B GLU* 1.3 79.5 - - - +
626B TYR* 1.3 60.3 + - + +
628B LYS* 3.2 29.1 + - - +
629B ILE* 2.9 39.7 + - + +
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Residues in contact with TYR 626 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B HIS* 3.4 42.7 - - + +
347B GLY* 2.6 36.3 + - - -
376B LEU* 3.5 31.4 - - + +
377B GLY* 3.6 14.4 - - - +
378B ALA* 3.9 8.1 - - + -
541B TYR* 4.7 0.9 + - - -
584B GLU* 3.6 25.1 + - - +
586B ILE* 4.1 5.0 + - - +
622B LEU* 2.9 52.2 + - + +
623B ARG 3.9 0.2 - - - +
625B ARG* 1.3 82.5 - - + +
627B TRP* 1.3 58.9 + - - +
629B ILE* 3.5 6.0 + - + +
630B ALA* 3.0 28.8 + - - +
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Residues in contact with TRP 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TYR* 3.3 27.6 - + - -
292B LEU* 3.6 27.1 - - + -
374B ARG 3.4 8.3 - - - -
375B TRP* 3.0 21.5 + - - -
376B LEU 3.8 4.9 - - - -
377B GLY* 3.3 13.2 - - - +
623B ARG* 3.1 41.7 + - + +
624B GLU* 4.1 3.8 - - - +
626B TYR* 1.3 74.2 - - - +
628B LYS* 1.3 66.7 + - - +
630B ALA* 3.3 6.0 + - + +
631B ASN* 3.0 26.1 + - - +
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Residues in contact with LYS 628 (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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574B ASP* 4.9 2.5 + - - -
577B ARG* 3.9 10.7 - - - +
624B GLU 3.1 13.4 + - - +
625B ARG* 3.4 48.2 + - - +
627B TRP* 1.3 76.7 - - - +
629B ILE* 1.3 71.5 + - - +
631B ASN* 3.2 15.2 + - - +
632B GLU* 3.3 22.4 + - + +
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Residues in contact with ILE 629 (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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344B TYR* 4.1 24.0 - - + -
346B HIS* 3.9 26.5 - - + -
577B ARG* 4.0 20.9 - - - +
584B GLU* 4.1 10.1 - - - +
625B ARG* 2.9 53.7 + - + +
626B TYR* 3.8 4.9 - - + +
628B LYS* 1.3 87.6 - - - +
630B ALA* 1.3 65.0 + - - +
632B GLU* 3.1 25.4 + - - +
633B THR 3.9 2.4 + - - -
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Residues in contact with ALA 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 3.8 48.2 - - + +
346B HIS* 4.1 12.1 - - - +
626B TYR 3.0 18.7 + - - +
627B TRP* 3.3 8.5 + - + +
629B ILE* 1.3 77.8 - - - +
631B ASN* 1.3 60.0 + - - +
632B GLU 3.5 0.3 + - - -
633B THR* 3.4 17.2 + - - -
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Residues in contact with ASN 631 (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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627B TRP 3.0 16.9 + - - +
628B LYS* 3.6 7.4 - - - +
629B ILE 3.1 0.6 - - - -
630B ALA* 1.3 74.0 - - - +
632B GLU* 1.3 63.8 + - - +
633B THR* 4.2 4.3 + - - -
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Residues in contact with GLU 632 (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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577B ARG* 2.9 36.0 + - - -
578B ARG* 2.9 32.5 + - - +
628B LYS* 3.3 20.3 + - + +
629B ILE* 3.1 18.3 + - - +
631B ASN* 1.3 80.0 - - - +
633B THR* 1.3 70.0 + - - +
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Residues in contact with THR 633 (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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292B LEU 5.5 1.2 + - - -
293B MET 6.1 0.4 - - - +
341B LYS* 6.2 4.7 - - - -
578B ARG* 4.2 15.3 + - - -
629B ILE 3.9 2.8 + - - -
630B ALA 3.4 17.5 + - - -
631B ASN* 3.5 4.3 + - - -
632B GLU* 1.3 85.6 - - - +
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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
------------------------------------------------------------
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