Contacts of the helix formed by residues 656 - 669 (chain A) in PDB entry 5HG1
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 ASN 656 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514A THR* 6.0 0.4 - - + +
602A PHE 3.8 9.2 - - - +
603A SER* 4.6 4.4 - - - +
604A PHE 4.7 3.8 + - - +
655A VAL* 1.3 76.3 - - - +
657A ASP* 1.3 83.0 + - - +
658A THR* 2.5 28.1 + - - +
659A VAL* 3.1 11.7 + - + +
660A GLY* 2.8 25.3 + - - -
683A ASN* 3.5 1.6 - - - +
706A ASN* 3.0 33.0 - - - +
708A GLU* 3.4 2.4 + - - -
1001A 62C 3.0 34.9 + - - -
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Residues in contact with ASP 657 (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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532A ASP* 5.3 0.2 - - - +
601A THR* 3.6 15.6 - - + +
603A SER* 3.3 21.0 - - - -
656A ASN* 1.3 81.0 - - - +
658A THR* 1.3 66.0 + - - +
661A THR* 2.7 29.7 + - - -
677A ILE* 3.7 12.5 - - + +
897A SER* 3.7 1.6 - - - +
1001A 62C 2.5 39.0 + - - -
1003A BG6 3.0 39.2 + - - +
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Residues in contact with THR 658 (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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656A ASN* 2.5 35.2 + - - +
657A ASP* 1.3 73.4 + - - +
659A VAL* 1.3 66.4 + - - +
661A THR* 3.0 2.8 + - - -
662A MET* 2.8 28.4 + - - +
675A GLY* 4.2 6.2 - - - +
677A ILE* 3.7 17.9 - - + +
683A ASN* 3.3 49.2 + - + +
684A ALA* 3.4 8.5 - - - +
685A CYS* 3.6 18.4 - - - +
706A ASN* 4.3 1.7 + - - -
1001A 62C 4.1 0.2 - - - +
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Residues in contact with VAL 659 (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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514A THR* 3.6 28.3 - - + -
516A VAL* 3.9 23.1 - - + -
655A VAL* 4.1 8.1 - - + -
656A ASN* 3.1 17.2 + - + +
658A THR* 1.3 87.6 + - - +
660A GLY* 1.3 63.9 + - - +
662A MET* 3.2 6.0 + - + +
663A MET* 3.0 22.5 + - - +
685A CYS* 3.7 11.4 - - + -
704A CYS* 3.8 18.2 - - - -
706A ASN* 4.8 1.1 - - + -
904A ILE* 3.8 20.4 - - + -
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Residues in contact with GLY 660 (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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655A VAL* 4.2 13.1 - - - +
656A ASN 2.8 18.2 + - - -
657A ASP 3.7 2.2 - - - -
659A VAL* 1.3 73.3 - - - +
661A THR* 1.3 55.2 + - - +
663A MET 3.4 0.5 + - - -
664A THR* 3.0 30.5 + - - -
897A SER* 3.7 23.6 - - - -
900A GLY* 3.4 6.6 - - - -
901A ALA 4.4 4.9 - - - -
904A ILE* 4.6 1.1 - - - -
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Residues in contact with THR 661 (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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657A ASP 2.7 22.1 + - - -
658A THR* 3.4 4.0 - - - +
660A GLY* 1.3 70.4 - - - +
662A MET* 1.3 66.1 + - - +
664A THR* 3.2 7.0 + - - -
665A CYS* 3.0 27.0 + - - +
676A LEU 4.5 2.7 - - - +
677A ILE* 3.7 14.1 - - - +
859A GLY* 3.6 31.0 - - - +
860A VAL 3.9 15.7 - - - +
861A ASP* 3.8 11.7 + - + +
893A SER* 4.6 4.7 + - - -
897A SER* 3.6 15.1 + - - +
1003A BG6 4.5 0.2 + - - -
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Residues in contact with MET 662 (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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516A VAL* 5.1 2.5 - - + -
658A THR 2.8 15.7 + - - +
659A VAL* 3.2 14.3 + - + +
661A THR* 1.3 74.8 - - - +
663A MET* 1.3 76.6 + - + +
665A CYS 3.5 0.2 + - - -
666A GLY* 2.9 25.8 + - - -
672A CYS* 3.7 13.1 - - - +
673A GLU* 3.7 26.0 - - - +
674A VAL 3.5 33.0 - - - +
675A GLY* 4.0 2.4 - - - -
685A CYS* 4.2 10.3 - - - +
687A MET* 3.9 18.8 - - - +
704A CYS* 3.7 27.1 - - + -
859A GLY* 5.0 0.4 - - - -
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Residues in contact with MET 663 (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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516A VAL* 4.5 9.9 - - + -
518A ALA 4.4 10.8 - - - +
519A THR* 5.2 2.7 - - - -
520A PRO* 3.3 41.1 - - + -
659A VAL 3.0 13.6 + - - +
662A MET* 1.3 89.8 - - + +
664A THR* 1.3 68.6 + - - +
666A GLY* 3.8 2.5 - - - +
667A PHE* 3.2 20.4 + - - +
900A GLY* 3.9 18.8 - - - +
903A LEU* 4.0 12.8 - - + +
904A ILE* 3.2 37.2 - - + +
907A VAL* 4.9 1.6 - - + -
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Residues in contact with THR 664 (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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660A GLY 3.0 12.7 + - - -
661A THR* 3.2 6.3 + - - -
663A MET* 1.3 78.5 - - - +
665A CYS* 1.3 62.0 + - - +
667A PHE* 3.5 14.9 + - - +
668A GLU* 4.1 7.6 + - - +
893A SER* 3.9 22.7 - - - +
895A ASP* 4.0 7.4 - - + -
896A GLY 3.0 22.1 + - - +
899A LYS* 3.8 26.9 + - + +
900A GLY* 3.0 26.1 + - - +
903A LEU* 4.6 5.2 - - - -
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Residues in contact with CYS 665 (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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661A THR* 3.0 13.9 + - - +
664A THR* 1.3 76.9 - - - +
666A GLY* 1.3 58.8 + - - +
668A GLU* 3.4 6.2 + - - +
669A ASP* 3.0 21.8 + - - +
672A CYS* 3.9 9.6 - - - -
859A GLY* 3.7 30.5 - - - -
860A VAL 4.4 1.1 - - - -
891A LEU* 3.7 36.9 - - + +
893A SER* 3.5 36.8 - - - -
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Residues in contact with GLY 666 (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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520A PRO* 6.1 3.8 - - - -
662A MET 2.9 17.0 + - - -
663A MET* 3.2 3.7 + - - -
665A CYS* 1.3 75.5 - - - +
667A PHE* 1.3 65.4 + - - +
669A ASP 3.1 29.3 - - - +
670A PRO* 3.6 7.7 - - - +
672A CYS* 3.8 10.3 - - - -
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Residues in contact with PHE 667 (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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520A PRO* 5.1 18.7 - - + +
545A VAL* 5.7 2.2 - - + -
552A GLY 4.6 12.1 - - - -
553A VAL* 3.3 43.1 - - + -
663A MET 3.2 5.4 + - - +
664A THR 3.6 11.7 - - - +
665A CYS 3.3 0.2 - - - -
666A GLY* 1.3 77.6 - - - +
668A GLU* 1.3 66.8 + - + +
670A PRO* 5.0 3.1 - - - +
899A LYS* 3.6 19.5 - - - +
903A LEU* 3.9 30.5 - - + -
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Residues in contact with GLU 668 (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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664A THR* 4.7 8.5 - - - +
665A CYS* 3.4 8.1 + - - +
666A GLY 3.2 0.2 - - - -
667A PHE* 1.3 90.5 - - + +
669A ASP* 1.3 58.4 + - + +
670A PRO* 3.5 9.0 - - - +
891A LEU* 3.6 27.7 - - + +
892A GLN 5.6 0.5 - - - +
893A SER* 4.8 11.8 - - - +
895A ASP* 5.1 3.5 - - - +
899A LYS* 4.6 9.4 + - - +
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Residues in contact with ASP 669 (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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665A CYS 3.0 12.5 + - - +
666A GLY* 3.1 17.9 - - - +
668A GLU* 1.3 77.6 - - + +
670A PRO* 1.3 66.2 - - - +
671A HIS* 3.0 25.2 + - - +
672A CYS* 3.2 9.0 + - - +
857A THR* 2.6 36.9 + - + +
889A SER* 5.2 1.7 - - - -
891A LEU* 4.2 13.9 - - + +
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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