Contacts of the strand formed by residues 475 - 480 (chain E) in PDB entry 4ZXB
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 PHE 475 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ASN* 4.4 5.6 - - - +
49D TYR* 4.9 0.2 - - - -
50D ALA* 3.6 9.3 - - - +
91D TYR* 3.0 20.7 + - - -
473E LEU* 5.3 6.3 - - + -
474E LYS* 1.3 73.4 - - - +
476E SER* 1.3 59.8 + - - +
477E TYR 4.5 0.2 - - - +
478E ILE* 4.4 24.0 - - + -
487E LEU* 3.8 28.5 - - + -
488E ARG 3.4 16.4 - - - +
489E TRP* 3.6 30.3 - + + -
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Residues in contact with SER 476 (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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34D TYR* 2.8 29.8 + - - -
46D ARG* 4.4 10.0 + - - -
49D TYR* 3.3 37.2 - - - -
91D TYR* 3.5 5.7 - - - -
474E LYS 3.5 2.8 + - - -
475E PHE* 1.3 72.8 - - - +
477E TYR* 1.3 60.6 + - - +
488E ARG* 3.0 29.6 + - - +
489E TRP* 3.6 7.3 + - - -
490E GLU* 5.6 0.2 - - - -
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Residues in contact with TYR 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASP* 2.8 28.7 + - - -
35C HIS* 2.7 35.7 + - - -
99C GLU* 3.9 39.3 - - + +
100C TRP* 4.0 12.1 - + - -
34D TYR* 3.4 17.5 - - - +
46D ARG* 5.9 0.9 - - - +
91D TYR* 4.2 1.6 - + - -
96D TRP* 3.8 5.6 - + - -
475E PHE 3.4 0.8 - - - -
476E SER* 1.3 83.0 + - - +
478E ILE* 1.4 74.7 + - - +
479E ARG* 3.4 25.2 - - + +
486E LEU* 4.0 11.7 - - + -
487E LEU* 3.2 5.4 - - - +
488E ARG* 2.9 46.7 + - + +
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Residues in contact with ILE 478 (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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32D ASN* 3.7 35.4 - - - +
91D TYR* 4.0 25.6 - - + +
92D SER 5.0 7.9 - - - +
96D TRP* 3.6 19.6 + - - -
475E PHE* 4.4 16.2 - - + -
477E TYR* 1.4 84.4 - - - +
479E ARG* 1.4 65.2 + - - +
480E THR* 5.2 8.1 - - + -
485E ILE* 4.9 4.9 - - + -
486E LEU 3.5 4.3 - - - -
487E LEU* 3.8 20.4 - - + -
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Residues in contact with ARG 479 (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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33C ASP* 2.7 38.2 + - - -
50C TRP* 2.9 45.6 - - - +
52C TYR* 3.8 19.8 - - - +
55C ASP* 5.8 1.4 + - - -
57C SER* 4.8 2.6 + - - -
96D TRP* 4.0 6.3 - - + -
477E TYR* 3.4 22.9 - - + +
478E ILE* 1.4 76.8 - - - +
480E THR* 1.3 74.4 + - - +
481E SER* 2.7 29.1 + - - -
484E LYS* 4.4 12.1 - - - +
485E ILE* 3.2 6.0 + - - -
486E LEU* 2.8 57.3 + - + +
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Residues in contact with THR 480 (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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50C TRP* 3.6 6.1 - - - -
59C LYS* 3.1 35.3 + - - +
94D SER* 4.2 13.2 + - - -
96D TRP* 5.2 1.2 - - - -
478E ILE* 5.2 9.6 - - + -
479E ARG* 1.3 86.2 - - - +
481E SER* 1.3 67.9 + - - +
484E LYS 3.8 2.7 - - - -
485E ILE* 4.3 19.5 - - + -
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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