Contacts of the helix formed by residues 513 - 524 (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 513 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511E SER 4.5 2.2 - - - +
512E TYR* 1.3 75.8 - - - +
514E GLU* 1.3 58.9 + - - +
515E TYR* 3.2 13.5 + - - +
516E ARG* 2.8 41.6 + - + +
517E TYR* 2.8 32.1 + - - +
563E TYR* 2.8 15.2 + - + +
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Residues in contact with GLU 514 (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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449D GLU* 4.9 14.3 - - + +
452D GLN* 3.1 28.9 + - - +
615D LYS* 6.0 1.5 + - - -
512E TYR* 3.4 38.6 + - + +
513E ASP* 1.3 71.4 + - - +
515E TYR* 1.3 61.0 + - - +
517E TYR* 3.7 0.3 - - - +
518E ARG* 3.0 67.1 + - - +
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Residues in contact with TYR 515 (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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449D GLU* 5.6 6.1 - - - +
450D ARG* 5.0 14.1 - - - -
513E ASP* 3.2 8.8 + - - +
514E GLU* 1.3 83.9 - - + +
516E ARG* 1.3 66.4 + - + +
518E ARG* 3.4 4.4 + - + +
519E SER* 3.1 36.3 + - - -
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Residues in contact with ARG 516 (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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513E ASP* 2.8 31.9 + - + +
515E TYR* 1.3 78.3 - - + +
517E TYR* 1.3 62.4 + - - +
519E SER* 3.4 7.7 + - - -
520E VAL* 3.1 28.6 + - + +
562E VAL 3.5 13.7 + - - -
563E TYR* 2.8 45.6 + - + -
564E LYS 3.7 7.7 + - - -
565E ASP* 3.2 31.4 + - - +
569E TYR* 3.8 5.5 + - - -
598E LYS* 5.1 3.6 - - - +
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Residues in contact with TYR 517 (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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503E LYS* 3.5 22.0 + - + -
506E ILE* 3.8 37.7 - - + +
507E ILE* 3.7 22.2 - - + -
512E TYR* 3.9 24.2 - + + -
513E ASP 2.8 17.8 + - - +
514E GLU 3.7 2.5 - - - +
516E ARG* 1.3 77.4 - - - +
518E ARG* 1.3 73.6 + - + +
520E VAL* 3.2 2.9 + - - +
521E ILE* 3.0 42.7 + - + +
530E ILE* 3.8 7.3 - - - +
537E ASP* 2.5 43.7 + - - -
563E TYR* 3.6 13.0 - + + -
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Residues in contact with ARG 518 (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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452D GLN* 6.5 0.4 - - - -
614D ASP* 4.9 14.8 + - - -
512E TYR* 4.7 3.4 + - - -
514E GLU* 3.0 53.2 + - - +
515E TYR* 3.9 4.9 - - + +
517E TYR* 1.3 85.2 - - + +
519E SER* 1.3 61.3 + - - +
521E ILE* 3.3 31.7 - - - +
522E LYS* 3.1 25.7 + - - +
527E GLU* 3.6 6.9 - - - +
530E ILE* 4.9 8.1 - - - +
536E LYS* 6.4 0.4 - - - +
537E ASP* 3.1 26.4 + - - -
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Residues in contact with SER 519 (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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515E TYR* 3.1 29.1 + - - -
516E ARG* 3.5 11.7 - - - -
517E TYR 3.2 0.2 - - - -
518E ARG* 1.3 76.7 - - - +
520E VAL* 1.3 58.2 + - - +
522E LYS* 3.5 8.4 + - - +
523E ALA* 3.0 29.6 + - - +
594E LEU* 4.2 23.1 - - - +
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Residues in contact with VAL 520 (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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506E ILE* 4.5 5.4 - - + -
516E ARG* 3.1 21.7 + - + +
517E TYR* 3.2 9.1 + - - +
519E SER* 1.3 77.0 - - - +
521E ILE* 1.3 58.4 + - + +
523E ALA 3.3 1.0 + - - -
524E CYS* 2.9 32.7 + - - +
559E ALA* 3.5 41.5 - - + +
562E VAL* 4.0 16.8 - - + +
563E TYR* 3.9 28.7 - - + +
594E LEU* 4.1 11.2 - - + -
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Residues in contact with ILE 521 (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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506E ILE* 4.1 12.8 - - + -
517E TYR* 3.0 36.6 + - + +
518E ARG* 3.3 47.6 - - - +
520E VAL* 1.3 77.2 - - + +
522E LYS* 1.3 60.5 + - - +
524E CYS 4.6 0.2 - - - +
525E GLN* 3.2 2.6 + - - -
526E LEU* 2.7 43.6 + - + -
527E GLU* 3.4 31.2 + - + +
530E ILE* 3.8 28.9 - - + -
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Residues in contact with LYS 522 (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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597D ASN* 3.3 24.9 + - - -
518E ARG 3.1 19.1 + - - +
519E SER* 3.5 8.5 - - - +
520E VAL 3.2 0.2 - - - -
521E ILE* 1.3 76.6 - - - +
523E ALA* 1.3 63.6 + - - +
525E GLN* 3.2 16.7 + - - +
527E GLU* 3.4 31.9 + - - +
589E SER* 5.1 0.7 + - - -
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Residues in contact with ALA 523 (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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519E SER 3.0 17.9 + - - +
520E VAL 3.9 2.0 - - - +
522E LYS* 1.3 75.6 - - - +
524E CYS* 1.3 60.0 + - - +
525E GLN* 3.3 2.0 + - - +
586E ILE* 4.0 6.9 - - - +
589E SER* 2.7 50.7 + - - +
590E CYS* 4.0 11.7 - - + +
594E LEU* 3.8 22.2 - - + -
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Residues in contact with CYS 524 (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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520E VAL* 2.9 21.4 + - - +
523E ALA* 1.3 75.7 - - - +
525E GLN* 1.3 61.3 + - - +
526E LEU* 3.4 11.3 + - + +
555E ARG* 3.0 43.6 - - + +
558E LEU* 3.9 15.9 - - + -
559E ALA* 3.9 23.1 - - + -
562E VAL* 4.9 1.3 - - - -
586E ILE* 3.8 8.2 - - + +
590E CYS* 3.9 27.6 - - - -
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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