Contacts of the helix formed by residues 558 - 575 (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 THR 558 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A LEU* 4.0 24.5 - - + -
544E GLU 5.1 0.2 - - - +
545E THR* 3.5 7.9 + - - +
549E PHE 3.3 12.3 - - - +
550E HIS 3.9 6.1 - - - -
551E GLN* 3.9 22.7 - - + +
554E PRO* 4.3 0.3 - - - +
555E LEU 2.6 30.4 + - - +
557E PHE* 1.3 83.0 - - - +
559E GLU* 1.3 64.0 + - - +
560E GLU* 3.6 12.1 + - - +
561E TYR* 3.1 16.3 + - - +
562E GLN* 3.2 16.1 + - - +
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Residues in contact with GLU 559 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D HIS* 2.8 21.7 + - - -
617D SER* 5.3 0.2 - - - +
545E THR* 3.7 20.4 - - + -
546E ILE 4.3 1.8 - - - +
547E ALA* 3.5 4.2 - - - -
548E GLY* 2.8 29.5 + - - +
549E PHE 3.0 18.6 + - - +
550E HIS* 4.2 18.4 + - + +
557E PHE 4.1 0.2 + - - -
558E THR* 1.3 72.3 - - - +
560E GLU* 1.3 58.4 + - - +
562E GLN* 3.3 5.0 + - - +
563E LYS* 3.0 34.2 + - + +
616E LYS* 4.5 4.9 - - + -
617E SER* 3.0 45.9 + - - +
618E ALA* 5.0 1.0 - - - +
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Residues in contact with GLU 560 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D PRO 3.6 5.9 - - - +
616D LYS 4.8 0.2 - - - -
617D SER* 4.7 2.9 + - - -
620D PHE* 3.4 37.9 - - + -
550E HIS* 2.6 38.2 + - - -
551E GLN 3.0 39.2 + - - +
552E ASP* 6.0 0.2 - - - +
554E PRO* 3.9 13.1 - - + +
558E THR* 3.1 4.2 - - - +
559E GLU* 1.3 80.4 + - - +
561E TYR* 1.3 56.2 + - - +
563E LYS* 3.4 12.0 + - + +
564E SER* 3.0 28.2 + - - -
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Residues in contact with TYR 561 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A GLN* 4.1 1.8 - - - -
506E SER* 2.8 37.7 + - - -
507E TRP* 4.0 19.5 - + - -
512E GLY* 3.2 28.7 - - - -
514E LEU* 3.5 35.1 - - + +
543E ALA* 4.3 11.7 - - + -
554E PRO* 3.8 11.1 - - + +
555E LEU* 3.1 38.8 - - - +
556E MET* 3.8 14.6 - - + -
557E PHE 4.5 0.4 - - - +
558E THR* 3.1 10.9 + - - +
559E GLU 3.3 0.2 - - - -
560E GLU* 1.3 76.0 - - - +
562E GLN* 1.3 61.2 + - - +
564E SER* 3.9 2.2 - - - +
565E LEU* 2.9 34.0 + - + +
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Residues in contact with GLN 562 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542E GLY* 6.1 0.4 - - - -
543E ALA* 3.9 20.0 + - + +
545E THR* 3.2 37.7 + - + +
558E THR 3.2 5.7 + - - +
559E GLU* 3.3 8.3 + - - +
561E TYR* 1.3 79.2 - - - +
563E LYS* 1.3 62.6 + - - +
565E LEU* 3.9 0.3 - - - +
566E LEU* 3.0 40.7 + - + +
586E ILE* 5.5 0.6 - - - +
606E LYS 3.5 13.1 + - - -
607E GLY 3.1 25.3 + - - -
608E ILE* 4.1 9.1 - - - +
616E LYS* 3.9 11.3 - - - +
618E ALA* 3.3 24.9 + - + +
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Residues in contact with LYS 563 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D LYS* 5.3 8.9 - - - +
617D SER* 5.7 3.1 + - - +
620D PHE* 5.8 8.9 - - + +
559E GLU* 3.0 19.8 + - + +
560E GLU* 3.6 13.9 - - + +
562E GLN* 1.3 76.4 - - - +
564E SER* 1.3 55.7 + - - +
566E LEU* 3.3 6.7 + - - +
567E GLU* 2.8 40.2 + - - +
617E SER* 4.2 26.6 + - - -
618E ALA* 3.9 22.0 - - + +
621E LEU* 3.8 25.1 - - + +
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Residues in contact with SER 564 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TRP* 4.3 9.7 - - - -
514E LEU* 3.2 32.4 - - - +
554E PRO* 4.7 5.2 - - - -
560E GLU 3.0 17.0 + - - -
561E TYR* 3.9 2.7 - - - -
562E GLN 3.3 0.2 - - - -
563E LYS* 1.3 73.1 - - - +
565E LEU* 1.3 66.5 + - - +
567E GLU* 3.2 16.2 + - - +
568E GLN* 2.9 35.3 + - - +
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Residues in contact with LEU 565 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504E TYR 5.4 0.7 - - - -
505E TYR 3.6 10.1 - - - +
506E SER* 3.5 22.9 - - - +
507E TRP* 4.3 7.2 - - + -
514E LEU* 3.6 13.9 - - + +
517E ILE* 4.0 9.9 - - + -
541E TYR* 4.2 1.1 - - + -
542E GLY* 3.6 41.3 - - - +
543E ALA* 4.1 6.5 - - + +
561E TYR* 2.9 28.2 + - + +
562E GLN 3.9 2.2 - - - +
564E SER* 1.3 76.8 - - - +
566E LEU* 1.3 74.9 + - + +
568E GLN* 3.3 1.2 + - - +
569E TYR* 3.0 40.8 + - + -
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Residues in contact with LEU 566 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541E TYR* 3.8 28.9 - - + -
542E GLY* 4.6 5.4 - - - -
562E GLN* 3.0 29.2 + - + +
563E LYS 3.5 4.7 - - - +
565E LEU* 1.3 88.0 - - + +
567E GLU* 1.3 57.7 + - - +
569E TYR* 3.1 2.1 + - - -
570E HIS* 2.8 53.6 + - + -
586E ILE* 3.6 25.4 - - + -
608E ILE* 4.6 1.3 - - + -
618E ALA* 4.0 35.4 - - + +
621E LEU* 4.1 7.0 - - + -
622E LEU* 4.8 3.4 - - + -
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Residues in contact with GLU 567 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563E LYS* 2.8 29.3 + - - +
564E SER* 3.5 18.6 + - - +
566E LEU* 1.3 74.1 - - - +
568E GLN* 1.3 70.0 + - - +
570E HIS* 3.3 9.4 + - - +
571E LEU* 3.1 30.0 + - + +
621E LEU* 3.6 26.0 - - + +
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Residues in contact with GLN 568 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514E LEU* 3.9 20.9 - - + +
515E GLU* 5.7 2.2 - - - -
517E ILE* 3.8 30.2 - - + +
518E GLN* 2.9 38.4 + - + +
564E SER* 2.9 29.0 + - - +
565E LEU 3.9 0.2 - - - +
567E GLU* 1.3 80.7 + - - +
569E TYR* 1.3 66.3 + - - +
571E LEU* 3.4 17.9 + - - +
572E GLY* 3.2 17.5 + - - -
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Residues in contact with TYR 569 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503E SER* 2.9 34.5 + - - -
504E TYR* 4.8 0.7 - - - -
505E TYR* 2.9 43.5 + + - -
517E ILE* 3.5 18.2 - - + -
521E LEU* 3.7 28.7 - - + +
538E GLN* 3.8 8.5 - - + -
541E TYR* 3.5 43.3 - + + -
565E LEU* 3.0 43.6 + - + +
566E LEU 3.6 3.4 - - - +
568E GLN* 1.3 75.4 - - - +
570E HIS* 1.3 59.2 + - + +
572E GLY* 3.2 2.3 + - - -
573E LEU* 2.9 36.3 + - + +
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Residues in contact with HIS 570 (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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541E TYR* 2.8 34.4 + + - -
566E LEU* 2.8 28.3 + - + +
567E GLU* 3.6 7.0 + - - +
568E GLN 3.2 0.2 - - - -
569E TYR* 1.3 79.3 - - - +
571E LEU* 1.3 56.6 + - + +
573E LEU* 3.2 3.3 + - + -
574E ASP* 2.8 37.3 + - - +
584E GLU* 4.0 4.0 - - - -
621E LEU* 3.6 27.2 - - + +
622E LEU* 3.5 22.8 - - + +
625E ARG* 3.4 42.8 + - - +
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Residues in contact with LEU 571 (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* 3.4 34.2 - - - +
567E GLU* 3.1 21.6 + - + +
568E GLN* 3.6 20.6 - - - +
569E TYR 3.3 0.2 - - - -
570E HIS* 1.3 76.6 - - + +
572E GLY* 1.3 60.9 + - - +
574E ASP* 3.4 26.9 - - + +
575E GLN* 3.5 15.1 + - - +
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Residues in contact with GLY 572 (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* 4.4 12.2 - - - +
521E LEU* 3.9 20.4 - - - -
522E ALA 5.9 1.3 - - - -
525E PHE* 4.3 10.2 - - - -
568E GLN 3.2 9.4 + - - -
569E TYR 3.7 3.1 - - - -
571E LEU* 1.3 76.9 - - - +
573E LEU* 1.3 64.9 + - - +
575E GLN* 3.1 22.5 + - - +
576E LYS* 3.9 2.6 + - - +
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Residues in contact with LEU 573 (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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344E TYR* 4.5 1.8 - - - +
521E LEU* 4.1 3.6 - - + +
525E PHE* 3.8 28.3 - - + -
538E GLN* 3.9 20.9 - - + -
541E TYR* 4.8 9.9 - - + -
569E TYR* 2.9 27.4 + - + +
570E HIS* 3.5 9.4 - - + +
572E GLY* 1.3 75.9 - - - +
574E ASP* 1.3 59.7 + - - +
576E LYS* 3.0 3.7 + - - -
577E ARG* 2.9 32.0 + - - +
581E VAL* 4.0 15.6 - - + +
584E GLU* 3.4 40.6 - - + +
625E ARG* 3.6 10.8 - - - +
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Residues in contact with ASP 574 (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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570E HIS 2.8 18.7 + - - +
571E LEU* 3.4 21.5 - - + +
572E GLY 3.2 0.2 - - - -
573E LEU* 1.3 77.0 - - - +
575E GLN* 1.3 66.2 + - - +
576E LYS 3.4 0.7 + - - -
577E ARG* 2.8 41.4 + - - +
578E ARG* 4.8 9.4 + - - -
579E LYS* 5.2 1.4 + - - -
625E ARG* 2.9 23.7 + - - -
628E LYS* 5.3 4.5 + - - -
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Residues in contact with GLN 575 (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* 5.7 3.1 - - - +
571E LEU 3.7 14.2 + - - +
572E GLY* 3.1 12.0 + - - +
573E LEU 3.1 1.4 - - - -
574E ASP* 1.3 81.0 - - - +
576E LYS* 1.3 79.4 + - + +
579E LYS* 2.8 28.4 + - - +
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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