Contacts of the strand formed by residues 501 - 511 (chain E) in PDB entry 5IXM
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 ASN 501 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491E LEU 4.0 4.7 - - - +
492E GLN* 3.0 40.7 + - + +
499E ALA 3.9 6.6 + - - -
500E VAL* 1.3 77.1 - - - +
502E LEU* 1.3 61.2 + - - +
526E PHE* 3.2 15.8 - - - -
527E ASN* 3.0 39.0 + - - +
528E ILE* 2.7 40.4 + - - +
543E GLN* 5.4 6.0 + - - +
544E MET* 5.3 8.8 - - + +
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Residues in contact with LEU 502 (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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491E LEU* 2.9 59.6 + - + +
500E VAL* 4.5 8.5 - - + +
501E ASN* 1.3 74.8 - - - +
503E GLY* 1.3 65.9 + - - +
524E ILE* 3.9 20.9 - - + -
525E GLY 3.5 16.2 - - - +
526E PHE* 5.0 5.8 - - + -
544E MET* 3.4 9.1 - - - +
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Residues in contact with GLY 503 (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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488E LEU* 6.5 0.2 - - - -
489E VAL 3.5 8.7 - - - -
502E LEU* 1.3 77.2 - - - +
504E TYR* 1.3 59.3 + - - -
505E GLU* 5.7 0.2 - - - -
523E LYS 4.2 0.2 - - - +
524E ILE* 3.2 8.9 - - - +
525E GLY 3.1 35.7 + - - +
544E MET* 3.9 12.1 - - - -
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Residues in contact with TYR 504 (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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487E GLN* 4.6 16.8 - - + -
488E LEU* 3.4 5.1 - - - +
489E VAL* 2.8 52.9 + - + +
503E GLY* 1.3 73.9 - - - +
505E GLU* 1.3 68.1 + - - +
506E ARG* 3.8 24.3 - - + -
522E ASN* 2.7 33.4 + - + -
523E LYS 3.5 17.3 - - - -
524E ILE* 4.0 21.3 - - + -
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Residues in contact with GLU 505 (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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486E SER* 5.8 2.0 - - - +
487E GLN 3.3 10.8 - - - +
488E LEU* 4.0 17.1 - - + +
503E GLY 5.7 0.4 - - - -
504E TYR* 1.3 82.3 - - - +
506E ARG* 1.3 62.9 + - - +
507E LYS* 2.6 41.9 + - + +
521E ASP 4.0 0.7 - - - +
522E ASN* 3.6 1.9 - - - -
523E LYS* 2.8 65.8 + - + +
547E SER* 3.7 13.1 + - - +
548E GLY* 3.6 18.0 - - - -
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Residues in contact with ARG 506 (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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484E PRO* 4.7 15.8 - - - +
485E ALA 4.7 0.3 - - - -
486E SER* 3.4 3.3 - - - -
487E GLN* 2.9 54.6 + - - +
504E TYR* 3.8 20.3 - - + +
505E GLU* 1.3 74.5 - - - +
507E LYS* 1.3 61.7 + - - +
520E TYR* 3.4 60.2 + - + +
521E ASP 3.6 8.1 - - - +
522E ASN* 3.5 25.3 + - - +
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Residues in contact with LYS 507 (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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124E THR* 4.4 14.3 - - + +
485E ALA 3.6 5.2 - - - +
486E SER* 4.3 3.8 - - - +
505E GLU* 2.6 37.4 + - + +
506E ARG* 1.3 75.1 - - - +
508E ILE* 1.3 65.3 + - - +
509E THR* 5.1 2.7 - - - -
520E TYR* 3.3 9.0 - - - -
521E ASP* 3.1 41.1 + - + +
523E LYS* 4.8 13.8 - - + +
547E SER 4.5 3.0 + - - -
548E GLY* 4.4 1.6 - - - -
549E ILE* 3.7 51.0 - - + +
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Residues in contact with ILE 508 (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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124E THR* 4.3 5.9 + - - -
478E ASP* 6.3 1.1 - - + -
483E GLN* 3.4 29.8 - - + +
484E PRO 3.7 9.4 - - - +
485E ALA* 2.9 33.3 + - + +
507E LYS* 1.3 77.5 - - - +
509E THR* 1.3 62.0 + - - +
510E GLY 4.0 8.7 - - - +
518E SER* 4.1 3.1 - - - -
519E LYS 3.7 5.6 - - - +
520E TYR* 3.6 22.2 - - + +
549E ILE* 4.1 9.4 - - - +
69F ILE* 4.3 5.8 - - + -
70F PHE 4.6 6.3 - - - +
71F ARG* 3.3 26.2 - - - +
73F GLY* 3.8 22.5 - - - +
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Residues in contact with THR 509 (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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115E THR* 4.3 20.0 + - + +
124E THR* 3.6 35.0 - - - +
507E LYS* 3.5 7.8 + - - -
508E ILE* 1.3 74.8 - - - +
510E GLY* 1.3 56.2 + - - +
519E LYS* 2.7 30.3 + - + +
520E TYR 3.9 2.2 - - - +
521E ASP* 3.2 38.0 + - - +
72F ASN 4.0 7.1 - - - +
73F GLY* 4.6 2.8 - - - -
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Residues in contact with GLY 510 (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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508E ILE* 4.0 0.2 - - - +
509E THR* 1.3 82.6 - - - +
511E TRP* 1.3 62.6 + - - +
518E SER* 3.7 1.7 - - - -
519E LYS* 2.9 34.4 + - - +
71F ARG 3.7 13.2 - - - +
72F ASN 3.4 13.6 + - - -
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Residues in contact with TRP 511 (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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450E TYR* 6.3 2.0 - + - -
510E GLY* 1.3 74.8 - - - -
512E ASN* 1.3 74.2 + - - +
513E ALA* 3.9 8.4 + - - +
516E GLN* 3.3 32.3 + - + -
517E THR* 3.2 35.2 - - - -
518E SER* 3.4 23.3 - - - -
519E LYS* 4.4 7.1 + - - +
71F ARG* 4.0 33.2 - - + -
72F ASN* 3.6 23.2 + - + +
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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