Contacts of the helix formed by residues 654 - 671 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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577C TYR* 3.9 4.7 + - - -
653C PHE* 1.3 76.5 - - - +
655C ALA* 1.3 64.1 + - - +
656C GLU* 3.4 15.5 + - - +
657C ARG* 3.3 25.1 + - - +
658C ARG* 3.1 24.1 + - - +
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Residues in contact with ALA 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654C SER* 1.3 73.0 - - - +
656C GLU* 1.3 57.8 + - - +
658C ARG* 3.8 22.8 - - - +
659C ASN* 2.9 44.7 + - - +
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Residues in contact with GLU 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C ARG* 5.1 9.0 + - - -
577C TYR* 2.7 31.7 + - + +
654C SER* 3.4 13.9 + - - +
655C ALA* 1.3 75.7 - - - +
657C ARG* 1.3 63.7 + - - +
659C ASN* 4.0 4.8 - - - +
660C SER* 2.9 30.3 + - - -
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Residues in contact with ARG 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C SER* 5.6 2.0 + - - -
576C GLY* 2.8 43.9 + - - +
577C TYR* 3.7 33.1 - - + -
648C ASP* 3.3 27.3 + - - +
652C GLN 5.6 0.2 + - - -
653C PHE* 3.3 51.1 - - + +
654C SER* 3.3 21.4 + - - +
655C ALA 3.3 0.2 - - - -
656C GLU* 1.3 80.1 - - - +
658C ARG* 1.3 59.5 + - - +
660C SER* 3.2 4.7 + - - -
661C ILE* 2.9 28.9 + - + +
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Residues in contact with ARG 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650C PHE* 3.6 46.2 + - + -
651C ASP* 4.8 5.6 + - - +
653C PHE* 2.9 38.3 + - + -
654C SER* 3.1 18.8 + - - +
655C ALA* 3.8 18.8 - - - +
657C ARG* 1.3 79.2 - - - +
659C ASN* 1.3 63.6 + - - +
661C ILE* 3.2 12.2 + - - +
662C LEU* 2.9 34.2 + - + +
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Residues in contact with ASN 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655C ALA* 2.9 34.0 + - - +
656C GLU* 4.0 5.3 - - - +
658C ARG* 1.3 76.8 + - - +
660C SER* 1.3 57.1 + - - +
662C LEU* 3.7 20.2 - - - +
663C THR* 2.7 39.7 + - - +
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Residues in contact with SER 660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C SER* 6.3 0.4 - - - -
550C GLY* 3.5 11.5 - - - +
551C GLY 3.2 20.8 + - - -
577C TYR* 2.8 37.0 + - - +
656C GLU 2.9 19.8 + - - -
657C ARG 3.4 5.2 - - - -
659C ASN* 1.3 74.9 - - - +
661C ILE* 1.3 58.1 + - - +
663C THR* 3.4 7.6 + - - -
664C GLU* 3.0 31.4 + - - +
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Residues in contact with ILE 661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576C GLY 3.9 18.4 - - - +
577C TYR 4.2 4.7 - - - -
578C LEU 3.6 19.1 - - - +
579C ASP* 3.8 21.8 - - + +
650C PHE* 4.2 17.3 - - + -
653C PHE* 4.0 28.9 - - + -
657C ARG* 2.9 20.7 + - + +
658C ARG* 3.2 6.7 + - - +
660C SER* 1.3 75.8 - - - +
662C LEU* 1.3 61.8 + - + +
664C GLU* 3.3 3.8 + - - +
665C THR* 3.0 29.1 + - - +
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Residues in contact with LEU 662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650C PHE* 6.4 2.5 - - + -
658C ARG* 2.9 24.1 + - + +
659C ASN* 3.8 20.6 - - - +
660C SER 3.4 0.2 - - - -
661C ILE* 1.3 75.5 - - + +
663C THR* 1.3 61.3 + - - +
665C THR* 3.3 10.1 + - - +
666C LEU* 2.9 40.2 + - + +
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Residues in contact with THR 663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C SER* 4.4 23.8 - - - +
659C ASN* 2.7 27.9 + - - +
660C SER* 3.6 9.1 - - - -
662C LEU* 1.3 72.4 - - - +
664C GLU* 1.3 61.4 + - - +
666C LEU* 3.4 13.2 + - + +
667C ARG* 2.8 29.6 + - + +
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Residues in contact with GLU 664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C SER* 4.1 6.8 + - - -
551C GLY* 3.4 16.1 + - - -
555C ARG* 2.6 36.6 + - - -
577C TYR 4.0 13.9 - - - +
578C LEU* 4.2 6.0 - - - +
579C ASP* 3.3 22.0 - - - +
582C THR* 4.1 4.0 - - - +
660C SER 3.0 20.3 + - - +
661C ILE 3.6 4.7 - - - +
662C LEU 3.3 0.2 - - - -
663C THR* 1.3 79.0 - - - +
665C THR* 1.3 63.7 + - - +
667C ARG* 2.8 36.6 + - - +
668C ARG* 3.2 26.2 + - - +
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Residues in contact with THR 665 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579C ASP* 3.5 20.0 - - - +
661C ILE* 3.0 18.6 + - - +
662C LEU* 3.3 15.1 + - + +
664C GLU* 1.3 75.9 - - - +
666C LEU* 1.3 60.9 + - - +
668C ARG* 3.2 10.1 + - - +
669C PHE* 3.2 41.7 - - + -
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Residues in contact with LEU 666 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662C LEU* 2.9 30.5 + - + +
663C THR* 3.6 12.1 - - + +
665C THR* 1.3 74.4 - - - +
667C ARG* 1.3 54.7 + - - +
669C PHE* 3.1 6.1 + - - +
670C SER* 2.7 47.5 + - - +
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Residues in contact with ARG 667 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525C GLN* 4.4 10.2 + - - -
528C GLU* 6.4 1.0 - - - +
529C ASP* 4.7 7.6 - - - -
552C GLN* 6.0 0.9 - - - +
555C ARG* 3.9 20.6 - - - +
582C THR* 3.1 30.3 + - - +
663C THR* 2.8 22.6 + - + +
664C GLU* 2.8 42.3 + - - +
666C LEU* 1.3 72.9 - - - +
668C ARG* 1.3 69.6 + - - +
670C SER* 4.1 4.7 - - - -
671C LEU* 2.8 44.6 + - - +
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Residues in contact with ARG 668 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525C GLN* 4.8 2.0 + - - -
579C ASP* 3.2 24.0 - - - -
581C LEU* 3.7 31.2 - - - +
582C THR* 3.1 20.5 + - - +
585C GLU* 2.7 44.8 + - - -
664C GLU 3.3 12.1 - - - +
665C THR* 3.2 11.4 + - - +
666C LEU 3.2 0.8 - - - -
667C ARG* 1.3 93.6 - - - +
669C PHE* 1.3 73.9 + - + +
671C LEU* 4.5 8.5 + - - +
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Residues in contact with PHE 669 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581C LEU* 5.3 13.0 - - + -
665C THR* 3.2 37.0 - - + +
666C LEU* 3.1 6.9 + - - +
668C ARG* 1.3 93.4 - - + +
670C SER* 1.3 60.9 + - - +
671C LEU* 5.1 4.8 - - - +
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Residues in contact with SER 670 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666C LEU* 2.7 30.0 + - - +
667C ARG* 4.1 3.1 - - - -
669C PHE* 1.3 76.6 - - - +
671C LEU* 1.3 78.3 + - - +
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Residues in contact with LEU 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528C GLU* 3.8 24.0 - - - +
667C ARG* 2.8 32.9 + - - +
668C ARG 4.8 9.0 - - - +
669C PHE 5.1 3.1 - - - +
670C SER* 1.3 95.8 + - - +
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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