Contacts of the helix formed by residues 654 - 671 (chain B) in PDB entry 1XMI
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 654 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577B TYR* 4.1 6.4 + - - -
652B GLN 3.6 2.7 + - - -
653B PHE* 1.3 77.2 - - - +
655B ALA* 1.3 65.3 + - - +
656B GLU* 3.6 10.3 + - - +
657B ARG* 3.2 25.6 + - - +
658B ARG* 3.0 23.0 + - - +
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Residues in contact with ALA 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653B PHE 3.9 0.2 + - - -
654B SER* 1.3 72.6 - - - +
656B GLU* 1.3 56.8 + - - +
658B ARG* 3.6 23.0 + - - +
659B ASN* 3.0 44.8 + - - +
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Residues in contact with GLU 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B GLY* 5.1 1.2 - - - -
553B ARG* 3.1 35.6 + - - -
577B TYR* 3.7 22.8 + - - -
654B SER* 3.7 9.3 + - - +
655B ALA* 1.3 77.2 - - - +
657B ARG* 1.3 59.7 + - - +
659B ASN* 3.5 4.4 + - - +
660B SER* 3.0 29.1 + - - -
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Residues in contact with ARG 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573B SER* 5.7 2.6 + - - -
576B GLY* 3.0 43.2 + - - +
577B TYR* 3.6 35.7 - - + -
648B ASP* 4.0 17.2 + - - -
653B PHE* 3.4 55.0 - - + +
654B SER* 3.2 21.2 + - - +
656B GLU* 1.3 78.1 - - - +
658B ARG* 1.3 62.8 + - - +
660B SER* 3.2 3.3 + - - -
661B ILE* 3.0 27.9 + - + +
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Residues in contact with ARG 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650B PHE* 3.6 45.1 + - + -
651B ASP* 4.2 12.5 + - - +
653B PHE* 2.7 36.9 + - + -
654B SER* 3.0 18.6 + - - +
655B ALA* 3.7 27.2 - - - +
657B ARG* 1.3 76.6 - - - +
659B ASN* 1.3 64.6 + - - +
661B ILE* 3.3 10.7 + - - +
662B LEU* 3.0 32.4 + - + +
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Residues in contact with ASN 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655B ALA* 3.0 30.5 + - - +
656B GLU* 4.0 4.9 - - - +
658B ARG* 1.3 77.9 + - - +
660B SER* 1.3 56.4 + - - +
662B LEU* 3.7 18.1 - - - +
663B THR* 2.7 39.9 + - - +
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Residues in contact with SER 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B GLY* 3.4 14.8 - - - +
551B GLY 3.3 17.7 + - - +
577B TYR* 2.7 39.0 + - - +
656B GLU* 3.0 15.8 + - - -
657B ARG 3.2 9.6 + - - -
659B ASN* 1.3 73.7 - - - +
661B ILE* 1.3 64.6 + - - +
663B THR* 3.3 7.3 + - - -
664B GLU* 3.0 26.0 + - - +
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Residues in contact with ILE 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B GLY 3.7 19.3 - - - +
577B TYR 4.1 6.5 - - - -
578B LEU 3.8 15.0 - - - +
579B ASP* 3.8 23.1 - - + +
580B VAL 5.4 0.4 - - - +
650B PHE* 4.3 13.2 - - + -
653B PHE* 3.8 31.2 - - + -
657B ARG* 3.0 22.8 + - + +
658B ARG* 3.3 8.7 + - - +
660B SER* 1.3 75.5 - - - +
662B LEU* 1.3 62.1 + - + +
664B GLU* 3.4 4.7 + - - +
665B THR* 3.0 28.5 + - - +
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Residues in contact with LEU 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650B PHE* 6.4 1.8 - - + -
658B ARG* 3.0 20.5 + - + +
659B ASN* 3.7 18.2 - - - +
661B ILE* 1.3 76.5 - - + +
663B THR* 1.3 58.9 + - - +
665B THR* 3.1 13.6 + - + +
666B LEU* 2.8 38.3 + - + +
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Residues in contact with THR 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B SER* 4.4 22.2 - - - -
659B ASN* 2.7 26.2 + - - +
660B SER* 3.5 8.3 - - - -
662B LEU* 1.3 76.1 - - - +
664B GLU* 1.3 61.5 + - - +
666B LEU* 3.3 14.8 + - + +
667B ARG* 2.8 29.2 + - + +
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Residues in contact with GLU 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549B SER* 3.5 13.9 + - - -
551B GLY* 3.4 23.5 + - - -
555B ARG* 2.5 32.4 + - - +
577B TYR 4.0 8.7 - - - +
578B LEU* 4.3 6.8 - - + +
579B ASP* 3.3 21.4 - - - +
582B THR* 4.6 0.9 - - - +
660B SER 3.0 19.6 + - - +
661B ILE 3.6 5.4 - - - +
663B THR* 1.3 77.0 - - - +
665B THR* 1.3 64.4 + - - +
667B ARG* 2.8 35.6 + - - +
668B ARG* 3.3 26.9 + - - +
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Residues in contact with THR 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B ASP* 3.5 18.8 - - + +
661B ILE* 3.0 18.0 + - - +
662B LEU* 3.1 17.9 + - + +
664B GLU* 1.3 74.1 - - - +
666B LEU* 1.3 64.9 + - - +
668B ARG* 3.3 9.4 + - - +
669B PHE* 3.2 41.2 - - + -
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Residues in contact with LEU 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662B LEU* 2.8 24.7 + - + +
663B THR* 3.5 17.0 - - + +
665B THR* 1.3 75.9 - - - +
667B ARG* 1.3 56.2 + - - +
669B PHE* 3.1 5.4 + - - +
670B SER* 2.9 44.5 + - - +
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Residues in contact with ARG 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B GLN* 4.0 19.4 + - - +
529B ASP* 4.6 10.6 + - - -
552B GLN* 5.9 1.6 - - - +
555B ARG* 3.6 25.8 - - - +
582B THR* 3.6 27.5 + - - +
663B THR* 2.8 21.3 + - + +
664B GLU* 2.8 39.0 + - - +
665B THR 3.3 0.2 - - - -
666B LEU* 1.3 73.3 - - - +
668B ARG* 1.3 66.6 + - - +
670B SER 4.6 0.2 - - - +
671B LEU* 3.2 46.9 + - + +
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Residues in contact with ARG 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B GLN* 4.8 2.8 + - - -
579B ASP* 3.3 23.6 - - - -
581B LEU* 3.6 27.3 - - - +
582B THR* 3.1 26.4 + - - +
585B GLU* 2.6 45.0 + - - -
664B GLU 3.3 13.0 + - - +
665B THR* 3.5 11.7 - - - +
667B ARG* 1.3 85.2 - - - +
669B PHE* 1.3 72.4 + - + +
671B LEU 4.1 7.7 - - - +
450C ARG* 3.3 25.3 - - - +
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Residues in contact with PHE 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581B LEU* 5.3 11.9 - - + -
665B THR* 3.2 35.9 - - + +
666B LEU* 3.1 7.7 + - + +
668B ARG* 1.3 94.5 - - + +
670B SER* 1.3 61.8 + - - +
671B LEU 4.8 0.7 - - - -
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Residues in contact with SER 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666B LEU* 2.9 30.0 + - - +
669B PHE* 1.3 80.9 - - - +
671B LEU* 1.3 76.7 + - - +
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Residues in contact with LEU 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B GLU* 4.6 19.7 - - - +
532B LYS* 4.1 24.5 - - - +
667B ARG* 3.2 35.1 + - + +
668B ARG 4.1 9.4 - - - +
669B PHE 4.8 0.7 - - - -
670B SER* 1.3 96.8 + - - +
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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