Contacts of the helix formed by residues 652 - 669 (chain A) in PDB entry 1Y8B
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 652 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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650A ILE* 5.8 0.9 - - + -
651A LEU* 1.3 76.3 - - - +
653A LYS* 1.3 67.9 + - - +
654A GLU* 2.8 16.8 + - - +
655A GLN* 2.9 47.2 + - - +
656A VAL* 3.4 10.2 + - - +
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Residues in contact with LYS 653 (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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651A LEU 3.8 2.6 + - - -
652A THR* 1.3 72.0 - - - +
654A GLU* 1.3 66.7 + - + +
656A VAL* 3.5 11.0 + - + +
657A GLN* 2.9 51.7 + - - +
660A LEU* 6.1 1.6 - - - +
698A PHE* 4.0 39.5 - - + -
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Residues in contact with GLU 654 (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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652A THR* 2.8 13.5 + - - +
653A LYS* 1.3 80.2 - - + +
655A GLN* 1.3 68.8 + - + +
657A GLN* 2.8 25.6 + - - +
658A ALA* 3.4 2.9 + - - +
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Residues in contact with GLN 655 (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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593A GLN* 5.4 3.6 - - - +
596A LEU* 6.0 0.2 - - - -
650A ILE 4.6 4.2 + - - -
651A LEU* 3.3 28.1 - - + +
652A THR* 2.9 45.9 + - - +
654A GLU* 1.3 74.2 - - + +
656A VAL* 1.3 65.2 + - - +
658A ALA* 2.8 24.3 + - - +
659A SER* 3.5 2.9 + - - -
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Residues in contact with VAL 656 (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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596A LEU* 4.5 11.4 - - + -
600A VAL* 5.1 1.6 - - + -
646A LEU* 4.3 14.1 - - + -
651A LEU* 3.6 26.7 - - + -
652A THR 3.7 8.3 - - - +
653A LYS* 3.8 11.2 - - + +
654A GLU 3.2 0.2 - - - -
655A GLN* 1.3 73.8 - - - +
657A GLN* 1.3 65.8 + - - +
659A SER* 2.5 37.9 + - - +
660A LEU* 3.0 27.9 + - + +
697A ILE* 4.2 23.3 - - + -
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Residues in contact with GLN 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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653A LYS* 2.9 36.6 + - - +
654A GLU* 2.8 23.3 + - - +
656A VAL* 1.3 73.8 - - - +
658A ALA* 1.3 59.3 + - - +
660A LEU* 4.1 18.6 - - - +
661A GLU* 2.9 46.9 + - + +
690A PHE* 5.2 8.7 - - - -
694A SER* 5.2 4.9 - - - -
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Residues in contact with ALA 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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654A GLU 3.4 2.5 + - - +
655A GLN* 2.8 14.0 + - - +
656A VAL 2.7 3.4 + - - -
657A GLN* 1.3 75.2 - - - +
659A SER* 1.3 54.2 + - - +
661A GLU* 3.2 6.3 + - - +
662A ASN* 2.7 38.7 + - - +
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Residues in contact with SER 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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596A LEU* 3.3 30.7 - - - +
597A ASP* 5.7 0.7 - - - -
600A VAL* 5.6 0.9 - - - -
655A GLN 3.5 2.5 + - - -
656A VAL* 2.5 33.9 + - - +
658A ALA* 1.3 75.3 - - - +
660A LEU* 1.3 68.5 + - - +
662A ASN* 3.1 1.2 + - - -
663A MET* 2.5 55.7 + - - +
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Residues in contact with LEU 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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600A VAL* 3.2 33.4 - - + -
604A LEU* 4.1 16.8 - - + -
653A LYS* 6.1 1.8 - - - +
656A VAL* 3.0 29.3 + - + +
657A GLN* 4.1 15.9 - - - +
659A SER* 1.3 89.3 + - - +
661A GLU* 1.3 56.5 + - - +
664A ALA* 2.5 39.6 + - + +
690A PHE* 5.1 6.3 - - + -
694A SER* 3.4 36.8 - - - +
697A ILE* 4.4 10.3 - - + -
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Residues in contact with GLU 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 GLN* 2.9 44.0 + - + +
658A ALA* 3.4 7.2 - - - +
660A LEU* 1.3 78.4 - - - +
662A ASN* 1.3 61.5 + - - +
664A ALA* 3.8 3.5 - - - +
665A LYS* 3.4 37.4 + - - +
690A PHE* 3.2 25.8 - - + -
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Residues in contact with ASN 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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658A ALA 2.7 21.4 + - - +
659A SER* 3.7 1.6 - - - +
661A GLU* 1.3 73.1 - - - +
663A MET* 1.3 92.3 + - - +
665A LYS* 3.1 10.9 + - - +
666A VAL* 3.0 31.8 + - - +
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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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597A ASP* 4.2 32.3 - - + +
600A VAL* 5.3 1.8 - - + -
601A GLN* 4.6 13.5 - - + +
604A LEU* 4.0 15.0 - - + -
623A ILE* 5.1 11.9 - - + -
659A SER* 2.5 57.7 + - - +
660A LEU* 4.4 0.2 - - - -
662A ASN* 1.3 95.9 - - - +
664A ALA* 1.3 53.9 + - - +
666A VAL* 2.9 10.0 + - + -
667A VAL* 2.5 45.4 + - + +
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Residues in contact with ALA 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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604A LEU* 4.1 12.0 - - + +
660A LEU 2.5 26.2 + - - +
661A GLU 3.8 5.2 - - - +
663A MET* 1.3 73.4 - - - +
665A LYS* 1.3 63.4 + - + +
667A VAL* 3.4 7.9 + - - +
668A ASP* 3.1 19.8 + - - +
690A PHE* 3.6 31.6 - - + -
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Residues in contact with LYS 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 GLU* 3.4 28.9 - - - +
662A ASN* 3.1 8.9 + - - +
663A MET 3.0 0.6 - - - -
664A ALA* 1.3 75.8 - - + +
666A VAL* 1.3 67.4 + - + +
667A VAL 3.0 1.3 - - - -
668A ASP* 3.0 21.4 + - - +
669A GLN* 3.6 3.6 + - - +
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Residues in contact with VAL 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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622A ASP 5.6 5.6 - - - +
623A ILE* 5.7 10.5 - - + -
662A ASN* 3.0 30.5 + - - +
663A MET* 2.9 12.7 + - + +
665A LYS* 1.3 78.7 - - + +
667A VAL* 1.3 61.2 + - + +
669A GLN* 3.3 31.9 + - - +
670A GLN* 4.4 2.8 + - - +
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Residues in contact with VAL 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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601A GLN* 4.4 19.7 - - + +
604A LEU* 3.8 20.9 - - + +
605A GLY* 3.5 18.6 - - - +
608A VAL* 4.0 11.1 - - + +
663A MET* 2.5 39.4 + - + +
664A ALA* 3.7 6.7 - - - +
666A VAL* 1.3 73.5 - - + +
668A ASP* 1.3 62.9 + - - +
669A GLN 3.0 6.0 + - - -
670A GLN* 3.0 42.9 + - - +
671A ASN* 4.2 1.2 + - - +
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Residues in contact with ASP 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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608A VAL* 6.0 6.1 - - - +
664A ALA 3.1 12.6 + - - +
665A LYS* 3.0 14.7 + - - +
667A VAL* 1.3 77.9 - - - +
669A GLN* 1.3 62.6 + - - +
670A GLN 3.1 0.4 - - - -
671A ASN* 3.2 15.9 + - - +
672A ALA* 3.2 19.3 + - - +
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Residues in contact with GLN 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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621A PRO* 5.3 12.1 - - + +
625A ASN* 5.1 10.1 + - - +
665A LYS 3.6 4.3 + - - +
666A VAL* 3.3 28.4 + - - +
667A VAL 3.0 0.4 - - - -
668A ASP* 1.3 80.1 - - - +
670A GLN* 1.3 64.1 + - + +
672A ALA* 2.8 20.7 + - + +
673A GLY* 3.2 10.5 + - - +
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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