Contacts of the helix formed by residues 616 - 632 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A THR* 2.9 33.7 + - + +
547A ALA* 4.6 15.0 - - + +
559A GLU* 4.2 7.2 - - + +
562A GLN* 3.9 18.2 - - - +
591A ASP* 2.7 39.8 + - - -
605A LYS 3.0 6.7 + - - -
607A GLY 2.7 26.1 + - - +
608A ILE* 2.8 17.2 + - - +
609A PHE 4.0 6.3 - - - -
610A THR* 4.3 15.7 - - + +
614A GLN 3.6 0.6 + - - -
615A PRO* 1.3 78.4 - - - +
617A SER* 1.3 67.2 + - - +
618A ALA 3.2 1.1 - - - +
619A ALA* 3.0 15.6 + - - +
620A PHE* 3.8 3.1 - - - -
550B HIS* 4.1 8.1 - - + -
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Residues in contact with SER 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A GLU* 3.0 23.6 + - - -
563A LYS* 3.9 26.7 - - - -
616A LYS* 1.3 71.2 - - - +
618A ALA* 1.3 61.0 + - - +
619A ALA 3.2 0.9 + - - -
620A PHE* 3.3 27.5 + - - +
621A LEU 3.7 2.9 + - - -
550B HIS* 3.7 10.2 - - - -
560B GLU* 4.7 1.0 + - - -
563B LYS* 4.6 6.7 + - - -
617B SER* 2.4 34.2 + - - -
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Residues in contact with ALA 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A GLU* 5.0 1.6 + - - +
562A GLN* 3.4 41.9 + - + +
563A LYS* 3.8 21.4 - - + +
566A LEU* 3.9 16.1 - - + +
608A ILE* 4.5 4.9 - - + -
616A LYS* 3.2 1.4 + - - +
617A SER* 1.3 75.5 - - - +
619A ALA* 1.3 66.1 + - - +
620A PHE 3.2 0.2 - - - -
621A LEU* 3.1 7.3 + - - +
622A LEU* 3.0 23.0 + - - +
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Residues in contact with ALA 619 (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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375A TRP* 4.4 6.5 - - + -
376A LEU* 3.7 5.5 - - - +
608A ILE* 3.5 35.6 + - + +
609A PHE* 4.4 10.5 - - + -
615A PRO* 3.5 18.6 - - + -
616A LYS 3.0 14.7 + - - +
618A ALA* 1.3 77.8 - - - +
620A PHE* 1.3 57.6 + - - +
622A LEU 3.3 1.2 + - - -
623A ARG* 2.9 30.8 + - - +
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Residues in contact with PHE 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A TRP* 3.7 23.6 - + - -
615A PRO* 3.8 27.4 - - + -
616A LYS 3.8 6.3 - - - -
617A SER* 3.6 14.6 - - - +
618A ALA 3.2 0.6 - - - -
619A ALA* 1.3 72.1 - - - +
621A LEU* 1.3 65.2 + - - +
623A ARG* 3.5 17.6 + - - +
624A GLU* 3.0 30.7 + - + +
552B ASP* 4.5 9.6 - - + -
560B GLU* 3.4 42.4 - - + -
563B LYS* 4.1 19.7 - - - +
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Residues in contact with LEU 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A LYS* 4.8 17.9 - - + +
566A LEU* 4.1 16.8 - - + -
567A GLU* 4.5 27.8 - - + +
570A HIS* 3.4 34.5 - - + +
617A SER 3.7 2.8 + - - +
618A ALA* 3.1 16.9 + - - +
620A PHE* 1.3 76.4 - - - +
622A LEU* 1.3 66.1 + - - +
624A GLU* 3.3 8.7 + - + +
625A ARG* 3.1 19.9 + - + +
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Residues in contact with LEU 622 (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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376A LEU* 4.3 6.1 - - + -
541A TYR* 3.6 11.7 - - - +
566A LEU* 4.5 3.4 - - + -
570A HIS* 3.4 30.7 - - + +
586A ILE* 3.6 36.3 - - + -
608A ILE* 3.8 16.6 - - + -
618A ALA 3.0 12.5 + - - +
619A ALA* 3.7 8.1 - - - +
621A LEU* 1.3 78.4 - - - +
623A ARG* 1.3 64.1 + - - +
625A ARG* 3.1 5.8 + - - +
626A TYR* 2.9 59.4 + - + +
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Residues in contact with ARG 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A TRP* 3.1 76.2 + - - +
376A LEU* 3.4 19.3 - - + +
619A ALA 2.9 17.3 + - - +
620A PHE* 3.5 17.8 + - - +
622A LEU* 1.3 76.5 - - - +
624A GLU* 1.3 80.9 + - - +
626A TYR 3.2 0.2 + - - -
627A TRP* 3.1 40.3 + - + +
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Residues in contact with GLU 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A PHE* 3.0 19.8 + - + +
621A LEU* 3.3 11.4 + - + +
623A ARG* 1.3 95.4 + - - +
625A ARG* 1.3 63.7 + - - +
627A TRP* 3.6 5.1 + - - +
628A LYS* 3.1 25.2 + - - +
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Residues in contact with ARG 625 (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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570A HIS* 3.3 55.2 + - - +
573A LEU* 3.6 10.1 - - - +
574A ASP* 2.9 35.0 + - - -
577A ARG* 3.7 9.9 - - - +
584A GLU* 2.9 38.4 + - - -
621A LEU* 3.1 12.8 + - + +
622A LEU* 3.1 10.3 + - - +
624A GLU* 1.3 76.6 - - - +
626A TYR* 1.3 63.2 + - + +
628A LYS* 3.2 9.7 + - - +
629A ILE* 2.8 44.7 + - + +
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Residues in contact with TYR 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A HIS* 3.3 42.7 - - + +
347A GLY* 2.6 34.3 + - - -
376A LEU* 3.5 26.2 - - + +
377A GLY* 3.5 20.9 - - - +
378A ALA* 3.9 6.7 - - + -
541A TYR* 4.6 1.0 + - - -
584A GLU* 3.6 27.8 + - - +
586A ILE 4.1 5.5 + - - -
622A LEU* 2.9 53.1 + - + +
625A ARG* 1.3 80.4 - - + +
627A TRP* 1.3 58.6 + - - +
629A ILE* 3.3 6.2 + - + +
630A ALA* 2.9 29.9 + - - +
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Residues in contact with TRP 627 (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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291A TYR* 3.5 26.2 - + - -
292A LEU* 3.7 26.0 - - + -
374A ARG 3.5 8.1 - - - -
375A TRP* 3.0 22.1 + - - -
376A LEU 3.7 7.6 - - - -
377A GLY* 3.3 12.8 - - - +
623A ARG* 3.1 41.4 + - + +
624A GLU* 4.1 4.7 - - - +
626A TYR* 1.3 73.0 - - - +
628A LYS* 1.3 67.7 + - - +
630A ALA* 3.2 7.8 + - + +
631A ASN* 3.0 25.1 + - - +
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Residues in contact with LYS 628 (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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624A GLU 3.1 19.5 + - - +
625A ARG* 3.4 8.5 - - - +
627A TRP* 1.3 75.9 - - - +
629A ILE* 1.3 61.8 + - + +
631A ASN* 3.2 14.4 + - - +
632A GLU* 3.4 26.3 + - + +
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Residues in contact with ILE 629 (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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344A TYR* 4.0 30.5 - - + -
346A HIS* 3.7 28.0 - - + -
577A ARG* 4.0 28.5 - - - +
584A GLU* 4.1 3.4 - - - +
625A ARG* 2.8 61.1 + - + +
626A TYR* 3.7 4.5 - - + +
628A LYS* 1.3 72.3 - - + +
630A ALA* 1.3 62.7 + - - +
632A GLU* 3.3 25.5 + - - +
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Residues in contact with ALA 630 (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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292A LEU* 3.9 47.4 - - + +
346A HIS* 4.2 10.1 + - - +
626A TYR 2.9 17.9 + - - +
627A TRP* 3.5 10.1 - - + +
629A ILE* 1.3 77.8 - - - +
631A ASN* 1.3 61.0 + - - +
632A GLU 3.5 4.5 + - - +
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Residues in contact with ASN 631 (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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627A TRP 3.0 16.2 + - - +
628A LYS* 3.8 7.2 - - - +
629A ILE 3.2 0.4 - - - -
630A ALA* 1.3 75.3 - - + +
632A GLU* 1.3 63.2 + - - +
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Residues in contact with GLU 632 (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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577A ARG* 3.0 35.4 + - - -
578A ARG* 2.9 32.7 + - - +
628A LYS* 3.4 25.0 + - + +
629A ILE* 3.3 17.6 + - - +
630A ALA 3.3 4.8 - - - +
631A ASN* 1.3 82.6 - - - +
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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
------------------------------------------------------------
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