Contacts of the strand formed by residues 518 - 527 (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 SER 518 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483E GLN* 3.3 27.4 + - - -
508E ILE* 4.1 11.2 - - - -
510E GLY 3.7 4.5 - - - -
511E TRP* 3.4 13.9 - - - +
517E THR* 1.3 88.3 + - - +
519E LYS* 1.3 64.4 + - - +
520E TYR* 3.8 17.5 + - - -
71F ARG* 2.9 27.7 + - - +
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Residues in contact with LYS 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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508E ILE* 3.6 2.5 - - - -
509E THR* 2.7 39.1 + - + +
510E GLY* 2.9 28.8 + - - +
511E TRP 4.6 6.1 + - - +
512E ASN* 3.4 52.8 - - + +
517E THR* 6.2 0.4 - - + -
518E SER* 1.3 73.5 - - - +
520E TYR* 1.3 58.5 + - - +
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Residues in contact with TYR 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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483E GLN* 3.2 33.5 + - - +
484E PRO* 2.4 36.1 + - + +
485E ALA 4.7 1.3 - - - -
506E ARG* 3.4 59.2 - - + +
507E LYS* 3.3 19.5 - - - -
508E ILE* 3.6 17.3 - - + -
509E THR* 3.9 1.1 - - - +
517E THR* 6.0 0.7 - - - -
518E SER* 3.8 19.0 + - - -
519E LYS* 1.3 78.2 - - - +
521E ASP* 1.3 74.6 - - - +
522E ASN* 5.1 3.1 + - - +
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Residues in contact with ASP 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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11E THR 4.6 2.7 - - - +
12E SER* 3.8 11.5 + - - +
13E ASN* 4.0 32.6 + - - +
115E THR* 5.0 3.5 - - - +
505E GLU 4.0 0.3 - - - +
506E ARG* 3.6 5.1 - - - +
507E LYS* 3.1 35.5 + - + +
509E THR* 3.2 27.3 + - + +
520E TYR* 1.3 84.1 - - - +
522E ASN* 1.3 66.8 + - - +
523E LYS* 5.5 2.4 - - + +
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Residues in contact with ASN 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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10E PHE* 4.1 3.4 - - + -
11E THR* 2.9 28.9 - - - +
12E SER* 2.8 21.3 + - - +
504E TYR* 2.7 33.1 + - + +
505E GLU 3.6 3.6 - - - -
506E ARG* 3.5 21.3 + - - +
520E TYR* 5.1 2.8 - - - +
521E ASP* 1.3 81.9 - - - +
523E LYS* 1.3 66.8 + - - +
524E ILE* 6.2 1.8 - - + -
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Residues in contact with LYS 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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9E LYS* 3.4 37.3 - - + +
10E PHE 3.2 4.9 - - - +
11E THR* 4.1 17.0 - - + +
118E THR* 4.4 19.2 + - - +
503E GLY 4.2 0.6 - - - +
504E TYR* 3.5 6.9 - - - -
505E GLU* 2.8 73.3 + - + +
507E LYS* 4.8 11.2 - - + +
521E ASP* 5.5 2.5 - - + +
522E ASN* 1.3 81.9 - - - +
524E ILE* 1.3 61.4 + - - +
525E GLY 4.3 0.2 - - - -
547E SER 5.6 2.0 + - - -
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Residues in contact with ILE 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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9E LYS* 3.4 3.1 - - - +
10E PHE* 2.9 56.1 + - + +
502E LEU* 3.9 21.3 - - + -
503E GLY 3.2 21.5 - - - +
504E TYR* 4.0 20.9 - - + -
522E ASN* 5.9 2.0 - - + -
523E LYS* 1.3 76.7 - - - +
525E GLY* 1.3 61.3 + - - +
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Residues in contact with GLY 525 (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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8E ALA 3.3 12.3 - - - -
9E LYS* 3.7 9.2 - - - +
502E LEU* 3.5 9.5 - - - +
503E GLY 3.1 33.4 + - - +
523E LYS 4.3 0.4 - - - -
524E ILE* 1.3 75.2 - - - +
526E PHE* 1.3 61.9 + - - -
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Residues in contact with PHE 526 (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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5E ILE* 5.4 7.6 - - + -
6E PRO 4.7 13.2 - - - -
7E ASN* 3.1 4.4 - - - +
8E ALA* 2.9 43.7 + - + +
500E VAL* 4.3 22.9 - - + -
501E ASN 3.2 31.4 - - - +
502E LEU* 5.0 6.7 - - + -
525E GLY* 1.3 74.4 - - - +
527E ASN* 1.3 80.8 + - - +
528E ILE* 4.4 10.3 - - + -
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Residues in contact with ASN 527 (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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6E PRO 5.0 0.9 - - - -
7E ASN* 3.4 27.7 - - + +
501E ASN* 3.0 34.9 + - - +
526E PHE* 1.3 86.0 - - - +
528E ILE* 1.3 65.9 + - - +
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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