Contacts of the helix formed by residues 579 - 590 (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 ASP 579 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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578C LEU* 1.3 77.7 - - - +
580C VAL* 1.3 63.2 + - - +
581C LEU* 3.4 16.5 + - - +
582C THR* 2.7 25.4 + - - -
583C GLU* 3.1 20.6 + - - +
661C ILE* 3.8 20.5 - - + +
664C GLU* 3.3 19.5 - - - +
665C THR* 3.5 27.0 + - - +
668C ARG* 3.2 26.7 - - - -
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Residues in contact with VAL 580 (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* 1.3 74.4 - - - +
581C LEU* 1.3 62.0 + - + +
583C GLU* 3.3 12.5 + - - +
584C LYS* 2.9 57.8 + - + +
606C LYS* 5.1 13.0 - - + +
661C ILE* 5.4 0.2 - - - +
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Residues in contact with LEU 581 (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* 3.4 10.5 + - - +
580C VAL* 1.3 81.1 - - + +
582C THR* 1.3 56.7 + - - +
584C LYS* 3.4 20.2 + - + +
585C GLU* 3.0 34.3 + - + +
668C ARG* 3.7 34.8 - - - +
669C PHE* 5.3 13.0 - - + -
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Residues in contact with THR 582 (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* 3.8 16.6 - - - +
555C ARG* 4.5 3.4 - - - +
578C LEU* 4.1 15.3 - - + -
579C ASP* 2.7 27.6 + - - -
580C VAL 3.4 0.4 - - - -
581C LEU* 1.3 73.2 - - - +
583C GLU* 1.3 65.5 + - - +
585C GLU* 3.8 3.2 - - - +
586C ILE* 3.0 40.3 + - + +
664C GLU* 4.1 2.7 - - - +
667C ARG* 3.1 27.2 + - - +
668C ARG* 3.1 15.5 + - - +
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Residues in contact with GLU 583 (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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575C PHE* 3.4 44.2 - - + +
578C LEU* 4.3 14.3 - - + +
579C ASP 3.1 18.2 + - - +
580C VAL* 3.7 12.8 - - - +
582C THR* 1.3 76.5 - - - +
584C LYS* 1.3 63.8 + - + +
586C ILE* 3.9 0.3 - - - +
587C PHE* 2.9 24.8 + - - +
606C LYS* 3.4 34.7 + - - +
609C HIS* 3.4 26.1 - - + +
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Residues in contact with LYS 584 (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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515A TYR* 5.6 0.2 + - - -
580C VAL* 2.9 37.5 + - + +
581C LEU* 3.4 23.7 - - + +
583C GLU* 1.3 78.3 - - + +
585C GLU* 1.3 62.7 + - + +
587C PHE* 3.9 7.1 - - - +
588C GLU* 3.2 23.0 + - - +
608C GLU* 3.3 30.1 + - + +
609C HIS* 5.5 3.1 - - - +
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Residues in contact with GLU 585 (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* 3.0 28.2 + - - +
581C LEU* 3.0 18.3 + - + +
582C THR* 3.8 2.1 - - - +
583C GLU 3.3 0.2 - - - -
584C LYS* 1.3 78.0 - - + +
586C ILE* 1.3 57.4 + - - +
588C GLU* 3.5 5.7 + - - +
589C SER* 2.9 32.0 + - - -
668C ARG* 2.7 46.5 + - - -
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Residues in contact with ILE 586 (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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523C ALA 4.0 7.9 - - - +
524C CYS* 3.9 9.2 - - + +
525C GLN* 3.9 19.5 - - + +
555C ARG* 3.8 34.1 - - + -
558C LEU* 3.6 31.0 - - + -
575C PHE* 3.7 11.9 - - + -
578C LEU* 4.2 8.7 - - + -
582C THR* 3.0 28.8 + - + +
583C GLU 4.3 0.4 - - - +
585C GLU* 1.3 71.1 - - - +
587C PHE* 1.3 61.6 + - - +
588C GLU 3.1 1.3 - - - -
589C SER* 3.5 4.0 - - - -
590C CYS* 2.7 38.9 + - + +
591C VAL* 3.5 0.3 + - - +
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Residues in contact with PHE 587 (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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453C LEU* 4.2 9.4 - - + -
575C PHE* 4.1 14.4 - + + -
583C GLU 2.9 18.5 + - - +
584C LYS* 3.9 5.4 - - - +
586C ILE* 1.3 75.1 - - - +
588C GLU* 1.3 63.9 - - - +
591C VAL* 3.2 30.9 + - + +
592C CYS* 3.0 48.0 + - - -
602C LEU* 3.7 27.1 - - + -
608C GLU* 4.6 5.2 - - + -
609C HIS* 3.5 50.7 - + + +
612C LYS* 3.9 22.2 - - + -
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Residues in contact with GLU 588 (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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515A TYR* 2.9 43.9 + - + +
519A SER* 6.0 0.2 - - - +
584C LYS 3.2 15.1 + - - +
585C GLU* 3.6 5.8 - - - +
586C ILE 3.1 0.6 - - - -
587C PHE* 1.3 87.2 - - + +
589C SER* 1.3 58.8 + - - +
592C CYS* 3.3 22.5 - - - +
593C LYS* 3.1 56.2 + - - +
612C LYS* 3.9 14.4 - - - +
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Residues in contact with SER 589 (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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593A LYS 6.0 1.6 - - - -
596A ALA* 6.0 3.7 - - - +
597A ASN* 4.0 2.8 - - - +
522C LYS 4.9 0.6 + - - -
523C ALA* 2.7 37.9 + - - +
525C GLN* 5.3 3.1 + - - +
585C GLU 2.9 22.8 + - - -
586C ILE* 3.5 5.4 - - - +
588C GLU* 1.3 73.5 - - - +
590C CYS* 1.3 58.3 + - - +
593C LYS* 3.6 13.0 - - - +
594C LEU* 3.2 24.6 + - - +
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Residues in contact with CYS 590 (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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523C ALA* 3.8 16.6 - - + +
524C CYS* 4.0 16.6 - - - -
558C LEU* 4.0 11.2 - - + -
562C VAL* 3.5 37.2 - - - -
586C ILE* 2.7 27.4 + - + +
589C SER* 1.3 73.4 + - - +
591C VAL* 1.3 67.3 + - + +
594C LEU* 3.4 10.5 + - - +
595C MET* 3.0 32.6 + - - +
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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