Contacts of the helix formed by residues 650 - 665 (chain A) in PDB entry 2MYS
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 SER 650 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475A PHE* 4.3 7.6 - - - -
479A CYS* 5.9 0.2 - - - -
533A PHE* 4.1 27.8 - - - -
537A GLU* 2.6 25.2 + - - +
599A ASN* 2.7 36.5 + - - -
648A THR* 3.5 1.4 + - - -
649A VAL* 1.3 78.0 - - - +
651A ALA* 1.3 61.5 + - - +
652A LEU 3.3 1.0 + - - -
653A PHE* 3.6 10.2 - - - +
654A ARG* 3.2 28.1 + - - +
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Residues in contact with ALA 651 (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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537A GLU* 3.9 11.7 - - - +
647A GLN* 3.9 13.6 + - + +
648A THR* 2.9 44.3 - - + +
650A SER* 1.3 78.6 + - - +
652A LEU* 1.3 61.6 + - - +
654A ARG* 4.1 9.7 + - - +
655A GLU* 3.7 17.8 + - - +
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Residues in contact with LEU 652 (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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647A GLN* 3.8 21.3 - - + +
648A THR 4.1 9.2 - - - +
649A VAL* 3.2 14.2 + - + +
651A ALA* 1.3 74.5 - - - +
653A PHE* 1.3 58.4 - - - +
654A ARG 2.8 2.5 - - - -
655A GLU* 2.3 45.6 + - + +
656A ASN* 2.6 35.2 + - - +
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Residues in contact with PHE 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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268A TYR* 5.5 9.6 - + + -
269A LEU* 3.6 31.0 - - + -
479A CYS* 3.2 57.2 - - + -
482A PHE* 4.2 7.2 - + - -
483A THR* 3.3 14.1 - - + -
533A PHE* 4.8 5.8 - + - -
649A VAL* 3.5 10.6 + - + +
650A SER* 3.6 14.6 - - - +
652A LEU* 1.3 76.4 - - - +
654A ARG* 1.3 59.3 + - + +
656A ASN* 3.4 7.1 + - + +
657A LEU* 2.7 58.2 + - + +
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Residues in contact with ARG 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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482A PHE* 4.7 10.8 - - + -
527A GLU* 3.9 26.1 + - + +
528A MLY 5.2 2.2 + - - -
529A PRO* 6.1 0.6 - - - +
533A PHE* 3.5 44.1 - - + +
534A SER* 4.9 9.5 + - - +
537A GLU* 2.9 34.0 + - - -
650A SER 3.2 16.5 + - - +
651A ALA* 4.1 11.3 + - - +
652A LEU 2.8 0.6 + - - -
653A PHE* 1.3 82.2 - - + +
655A GLU* 1.3 48.7 + - - +
657A LEU* 3.0 7.3 + - - +
658A ASN* 2.6 47.0 + - - +
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Residues in contact with GLU 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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647A GLN* 4.4 8.9 + - - -
651A ALA 3.7 10.2 + - - +
652A LEU* 2.3 41.9 + - + +
654A ARG* 1.3 72.0 - - - +
656A ASN* 1.3 64.9 + - - +
658A ASN* 3.4 7.0 + - - +
659A MLY 3.2 23.9 + - - +
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Residues in contact with ASN 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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266A GLU* 4.6 4.7 - - - +
267A THR 5.4 2.5 - - - +
268A TYR* 4.2 24.3 + - + -
652A LEU* 2.6 36.2 + - - +
653A PHE* 3.8 7.5 + - + +
655A GLU* 1.3 76.4 + - - +
657A LEU* 1.3 58.1 + - - +
658A ASN 3.0 9.5 + - - -
659A MLY 3.1 31.8 + - - +
660A LEU* 3.0 23.9 + - - +
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Residues in contact with LEU 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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268A TYR* 5.0 2.4 - - - -
482A PHE* 3.5 39.5 - - + -
483A THR* 3.9 31.2 - - + +
486A MLY 4.3 11.6 - - + -
653A PHE* 2.7 41.5 + - + +
654A ARG* 3.3 7.9 - - - +
656A ASN* 1.3 72.3 - - - +
658A ASN* 1.3 61.4 + - - +
660A LEU* 3.9 16.8 - - + -
661A MET* 3.4 31.3 + - + +
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Residues in contact with ASN 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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486A MLY 3.1 34.6 - - - -
527A GLU* 5.0 1.8 + - - -
654A ARG* 2.6 31.0 + - - +
655A GLU* 3.7 8.3 - - - +
656A ASN 3.0 0.4 - - - -
657A LEU* 1.3 78.0 - - - +
659A MLY 1.3 63.1 + - - +
660A LEU 2.9 4.5 - - - -
661A MET* 3.5 2.6 + - - +
662A ALA* 3.1 26.0 + - - +
665A ARG* 5.6 0.7 + - - -
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Residues in contact with MLY 659 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A GLU* 2.5 42.9 + - - +
655A GLU 3.2 15.4 + - - +
656A ASN* 3.5 27.1 - - - +
658A ASN* 1.3 78.3 + - - +
660A LEU* 1.3 58.8 + - - +
662A ALA* 3.8 6.7 - - - +
663A ASN* 3.3 33.7 + - - +
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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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249A PHE* 3.9 28.5 - - + -
266A GLU* 6.0 0.2 - - - -
268A TYR* 3.5 35.7 - - + +
462A LEU* 4.3 17.3 - - + -
464A ILE* 4.5 9.2 - - + -
483A THR* 5.2 2.7 - - + -
487A LEU* 5.5 2.9 - - + -
656A ASN 3.0 16.3 + - - +
657A LEU* 3.8 21.5 - - + +
659A MLY 1.3 75.7 + - - -
661A MET* 1.3 55.0 + - + +
662A ALA 2.9 3.6 - - - -
663A ASN* 2.8 26.9 + - - +
664A LEU* 2.8 36.5 + - + +
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Residues in contact with MET 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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486A MLY 4.2 28.9 - - + +
487A LEU* 3.6 36.3 - - + -
490A PHE* 4.1 30.5 - - + -
657A LEU* 3.4 29.9 + - + +
658A ASN* 3.5 3.3 + - - +
660A LEU* 1.3 79.2 - - + +
662A ALA* 1.3 57.4 + - - +
664A LEU* 3.5 14.8 - - + +
665A ARG* 3.1 53.6 + - - +
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Residues in contact with ALA 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 ASN 3.1 19.7 + - - +
659A MLY 3.8 7.2 - - - +
660A LEU 2.9 0.6 - - - -
661A MET* 1.3 74.7 - - - +
663A ASN* 1.3 66.8 + - - +
664A LEU 3.1 1.3 - - - -
665A ARG* 3.3 21.5 + - - +
666A SER* 3.1 17.2 + - - -
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Residues in contact with ASN 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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249A PHE* 4.2 21.9 - - + -
251A ARG* 3.6 36.3 + - - +
458A PHE* 4.3 11.5 - - + -
659A MLY 3.3 24.7 + - - +
660A LEU* 2.8 10.4 + - - +
662A ALA* 1.3 80.4 - - - +
664A LEU* 1.3 61.7 + - - +
665A ARG 3.4 0.3 + - - -
666A SER* 3.7 11.5 + - - -
667A THR* 2.7 21.1 + - - -
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Residues in contact with LEU 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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174A SER* 4.7 14.6 - - - +
176A LEU* 4.4 12.1 - - + -
249A PHE* 4.0 29.4 - - + -
462A LEU* 4.7 5.8 - - + -
487A LEU* 3.9 15.7 - - + -
490A PHE* 3.3 34.6 - - + -
660A LEU* 2.8 28.3 + - + +
661A MET* 3.5 35.2 - - + +
663A ASN* 1.3 79.3 - - - +
665A ARG* 1.3 55.0 + - - +
667A THR* 2.8 24.0 - - - +
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Residues in contact with ARG 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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486A MLY 4.8 17.6 - - - -
489A GLN* 5.8 2.4 + - - -
490A PHE* 4.3 18.5 - - + -
658A ASN 5.6 0.6 + - - -
661A MET* 3.1 49.1 + - + +
662A ALA* 3.3 14.4 + - - +
663A ASN 3.2 0.8 - - - -
664A LEU* 1.3 74.0 - - - +
666A SER* 1.3 53.1 - - - +
667A THR 2.6 24.7 + - - +
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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