Contacts of the helix formed by residues 579 - 590 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474B GLU* 2.6 28.3 - - - +
578E LEU* 1.3 76.1 - - - +
580E VAL* 1.3 64.6 + - - +
581E LEU 3.3 6.4 + - - -
582E THR* 2.6 26.0 + - - -
583E GLU* 3.1 20.6 + - - +
661E ILE* 3.8 20.7 - - + +
664E GLU* 3.3 20.8 - - - +
665E THR* 3.5 22.2 - - - +
668E ARG* 3.2 16.8 - - - -
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Residues in contact with VAL 580 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ATP 5.9 2.2 - - - +
401B TRP* 4.3 20.0 - - + +
403B GLU* 6.3 0.7 - - - -
474B GLU* 3.4 33.2 + - + +
578E LEU 4.0 0.2 + - - -
579E ASP* 1.3 73.7 - - - +
581E LEU* 1.3 59.9 + - + +
583E GLU* 3.5 14.6 + - - +
584E LYS* 3.0 57.2 + - + +
606E LYS* 5.5 7.4 - - - +
661E ILE* 5.5 0.4 - - - +
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Residues in contact with LEU 581 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B MET 3.8 19.7 - - - +
473B GLY* 3.6 20.2 - - - +
474B GLU* 3.1 26.3 + - - +
579E ASP* 3.3 7.4 - - - +
580E VAL* 1.3 75.6 - - + +
582E THR* 1.3 61.3 + - - +
584E LYS* 3.3 18.2 + - + +
585E GLU* 3.0 34.4 + - + +
668E ARG* 3.7 32.1 - - - +
669E PHE* 5.2 3.4 - - + -
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Residues in contact with THR 582 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525E GLN* 3.7 14.8 - - - +
555E ARG* 4.8 2.2 - - - -
578E LEU* 4.0 15.5 - - + -
579E ASP* 2.6 27.7 + - - -
581E LEU* 1.3 73.6 - - - +
583E GLU* 1.3 60.9 + - - +
585E GLU* 3.4 3.4 + - - +
586E ILE* 2.9 47.2 + - + +
664E GLU* 4.3 2.2 - - - +
667E ARG* 3.1 27.8 + - - +
668E ARG* 3.2 15.6 + - - +
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Residues in contact with GLU 583 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575E PHE* 3.3 42.3 - - + +
578E LEU* 4.2 16.5 - - + +
579E ASP 3.1 16.7 + - - +
580E VAL* 3.6 14.2 - - - +
582E THR* 1.3 76.6 - - - +
584E LYS* 1.3 58.6 + - + +
586E ILE 3.8 0.2 - - - -
587E PHE* 2.8 33.3 + - - +
606E LYS* 3.6 35.4 + - - +
609E HIS* 3.5 21.7 - - + +
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Residues in contact with LYS 584 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B GLU* 4.0 23.4 + - - +
473B GLY 5.7 0.6 + - - -
474B GLU 5.5 0.2 + - - -
476B GLU* 4.0 26.9 + - - +
580E VAL* 3.0 43.0 + - + +
581E LEU* 3.6 18.7 - - + +
582E THR 3.3 0.2 - - - -
583E GLU* 1.3 78.8 - - + +
585E GLU* 1.3 63.6 + - + +
587E PHE* 3.6 7.8 + - - +
588E GLU* 3.1 23.7 + - - +
608E GLU* 3.7 28.2 + - + +
609E HIS* 5.5 3.1 - - - +
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Residues in contact with GLU 585 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525E GLN* 2.8 28.2 + - - +
581E LEU* 3.0 17.9 + - + +
582E THR* 3.8 0.8 - - - +
584E LYS* 1.3 78.9 - - + +
586E ILE* 1.3 56.8 + - - +
588E GLU* 3.5 5.5 + - - +
589E SER* 2.9 32.1 + - - -
668E ARG* 2.8 43.8 + - - -
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Residues in contact with ILE 586 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523E ALA 4.0 12.6 - - - +
524E CYS* 3.8 9.2 - - + +
525E GLN* 4.0 15.0 - - + +
555E ARG* 3.7 28.7 - - + -
558E LEU* 3.7 31.0 - - + -
575E PHE* 3.8 9.6 - - + -
578E LEU* 4.3 7.6 - - + -
582E THR* 2.9 38.1 + - + +
583E GLU 4.3 1.1 - - - +
585E GLU* 1.3 73.8 - - - +
587E PHE* 1.3 67.6 + - - +
588E GLU 3.2 0.2 - - - -
589E SER* 3.6 4.3 - - - -
590E CYS* 2.8 31.5 + - + +
591E VAL* 3.6 0.3 + - - +
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Residues in contact with PHE 587 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453E LEU* 4.3 6.5 - - + -
575E PHE* 4.2 12.0 - + + -
583E GLU 2.8 19.8 + - - +
584E LYS* 3.7 5.8 - - - +
586E ILE* 1.3 74.4 - - - +
588E GLU* 1.3 67.4 + - - +
591E VAL* 3.2 24.4 + - + +
592E CYS* 3.0 52.5 + - - -
602E LEU* 3.6 28.0 - - + -
608E GLU* 4.4 6.3 - - + -
609E HIS* 3.5 54.5 - + + +
612E LYS* 3.9 20.6 - - + -
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Residues in contact with GLU 588 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584E LYS 3.1 15.3 + - - +
585E GLU* 3.6 5.8 - - - +
587E PHE* 1.3 89.3 - - - +
589E SER* 1.3 58.9 + - - +
592E CYS* 3.3 18.1 - - - +
593E LYS* 3.1 56.1 + - - +
612E LYS* 3.6 34.0 + - - -
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Residues in contact with SER 589 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522E LYS 5.5 0.2 - - - -
523E ALA* 2.7 39.0 + - - +
525E GLN* 5.6 1.9 + - - +
585E GLU 2.9 22.7 + - - -
586E ILE* 3.6 3.3 - - - +
588E GLU* 1.3 73.7 - - - +
590E CYS* 1.3 58.5 + - - +
593E LYS* 3.6 12.9 - - - +
594E LEU* 3.2 24.1 + - - +
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Residues in contact with CYS 590 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523E ALA* 4.0 15.3 - - + +
524E CYS* 3.9 16.6 - - - -
558E LEU* 4.0 9.9 - - + -
562E VAL* 3.5 37.9 - - - -
586E ILE* 2.8 32.6 + - + +
589E SER* 1.3 73.7 + - - +
591E VAL* 1.3 63.3 + - + +
592E CYS 3.4 0.2 - - - -
594E LEU* 3.3 5.0 + - - +
595E MET* 3.0 36.5 + - - +
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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