Contacts of the strand formed by residues 473 - 477 (chain 3) in PDB entry 5Z58
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 TYR 473 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4603 TRP 3.4 0.9 - - - +
4613 THR* 2.9 10.0 - - - +
4623 VAL* 2.8 41.0 + - + +
4643 ARG* 2.5 45.2 + - - -
4723 ALA* 1.3 84.1 - - + +
4743 ILE* 1.3 62.4 + - - +
4753 ILE* 3.7 9.9 - - + -
4843 VAL* 4.3 0.9 - - + -
4853 LEU 3.4 15.3 - - - -
4863 SER* 3.9 10.8 - - - -
4973 SER* 3.3 44.8 + - - -
4993 PHE* 3.2 45.2 - + + -
5163 LEU* 4.1 16.4 - - + -
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Residues in contact with ILE 474 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4593 VAL* 4.2 1.1 - - + -
4603 TRP 3.1 2.9 - - - -
4613 THR* 4.3 1.3 - - - +
4723 ALA 3.9 1.2 + - - -
4733 TYR* 1.3 75.8 - - - +
4753 ILE* 1.3 61.4 + - - +
4763 VAL* 4.8 0.2 - - + -
4853 LEU* 2.7 55.7 + - + +
4873 ILE* 4.1 8.5 - - + +
4913 VAL* 3.8 26.5 - - + -
7453 PHE* 3.6 32.8 - - + -
7553 VAL* 3.8 28.0 - - + -
7623 LEU* 3.9 22.2 - - + -
7643 ILE* 3.7 19.7 - - + -
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Residues in contact with ILE 475 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4593 VAL* 3.1 8.0 - - - -
4603 TRP* 2.9 37.0 + - + +
4623 VAL* 5.4 0.2 - - + -
4733 TYR* 3.7 13.9 - - + -
4743 ILE* 1.3 85.0 - - - +
4763 VAL* 1.3 63.0 + - - +
4773 SER 3.7 0.3 + - - -
4823 THR* 4.2 14.4 - - + +
4833 LEU 3.9 3.6 - - - +
4843 VAL* 3.5 20.4 - - + -
4853 LEU 3.5 2.7 - - - +
4993 PHE* 3.3 39.0 - - + -
5053 THR* 4.2 9.2 - - - +
5083 CYS* 3.8 31.2 - - + -
5183 GLN* 3.9 9.2 - - - +
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Residues in contact with VAL 476 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4523 LEU* 3.5 25.1 - - + -
4593 VAL* 4.1 4.5 - - + -
4743 ILE 4.8 0.2 - - - +
4753 ILE* 1.3 71.8 - - - +
4773 SER* 1.3 61.0 + - - +
4783 PHE* 3.4 34.2 + - + -
4813 ALA 4.1 0.2 - - - +
4823 THR* 2.8 27.2 - - - -
4833 LEU* 2.8 28.1 + - + +
4853 LEU* 3.6 23.8 - - + -
7573 ILE* 4.6 5.4 - - + -
7623 LEU* 3.5 28.0 - - + -
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Residues in contact with SER 477 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4563 PRO* 3.6 2.9 - - - +
4573 ASN* 2.4 53.0 + - - +
4583 ALA* 2.9 35.2 + - - +
4603 TRP* 3.8 11.9 - - - -
4753 ILE 3.7 1.4 + - - -
4763 VAL* 1.3 70.7 - - - +
4783 PHE* 1.3 54.0 + - - +
4823 THR* 3.5 13.2 - - - -
5043 PRO* 3.3 5.2 - - - +
5053 THR 3.1 22.5 + - - -
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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