Contacts of the strand formed by residues 922 - 928 (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 GLY 922 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9103 ALA* 4.2 1.2 - - - -
9113 LYS* 2.9 28.8 + - - +
9203 VAL* 3.3 16.3 - - - +
9213 ALA* 1.3 80.1 - - - +
9233 GLY* 1.3 57.4 + - - -
9243 PHE* 5.1 1.1 - - - -
9453 VAL 4.3 1.1 - - - -
9463 GLU* 3.4 21.8 - - - -
9473 GLU 4.5 2.0 - - - -
9483 VAL 4.7 2.1 + - - -
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Residues in contact with GLY 923 (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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9093 VAL 3.6 9.0 - - - -
9103 ALA* 4.5 0.9 - - - -
9113 LYS* 4.1 2.0 - - - +
9223 GLY* 1.3 73.9 - - - -
9243 PHE* 1.3 79.4 + - - -
9453 VAL* 2.6 40.4 + - - +
9473 GLU 3.5 15.8 + - - -
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Residues in contact with PHE 924 (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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8863 GLU* 4.1 16.8 - - + -
9093 VAL* 2.8 36.8 + - + +
9103 ALA 5.4 0.4 - - - -
9113 LYS* 3.6 40.2 - - + -
9223 GLY* 5.7 0.7 - - - -
9233 GLY* 1.3 92.9 - - - -
9253 VAL* 1.3 68.8 + - - +
9263 TYR* 4.3 18.4 - - + -
9423 LYS* 3.5 29.6 - - + -
9433 THR 3.5 5.2 - - - +
9443 PRO* 3.5 30.3 - - + -
9453 VAL* 3.5 3.9 - - - +
9493 PRO* 4.1 1.6 - - - +
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Residues in contact with VAL 925 (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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9063 LEU* 5.1 6.5 - - + -
9073 VAL 3.6 12.8 - - - +
9083 GLY* 4.4 10.3 - - - +
9243 PHE* 1.3 80.9 - - - +
9263 TYR* 1.3 77.5 + - - +
9273 THR* 4.6 4.4 + - - +
9413 HIS 3.8 1.2 - - - +
9433 THR* 2.9 52.0 + - + +
9453 VAL* 4.6 11.4 - - + -
9493 PRO* 4.5 9.9 - - + -
9523 ILE* 5.1 2.5 - - + -
9613 ILE* 4.6 20.0 - - + -
9773 LEU* 4.4 15.0 - - + -
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Residues in contact with TYR 926 (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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8823 LEU* 4.3 24.5 - - + -
8833 GLU* 4.8 1.1 - - - +
8863 GLU* 2.2 41.8 + - - -
9063 LEU* 3.6 2.6 - - - -
9073 VAL* 2.9 35.8 + - + +
9093 VAL* 3.6 29.2 - - + -
9243 PHE* 4.3 11.0 - - + +
9253 VAL* 1.3 79.1 - - - +
9273 THR* 1.3 65.4 + - - +
9283 TYR* 3.6 31.4 - + + +
9393 PHE* 3.9 18.8 - + + -
9413 HIS 3.9 2.0 - - - -
9423 LYS* 3.4 35.9 + - + +
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Residues in contact with THR 927 (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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9043 TYR* 4.4 12.8 - - + -
9053 VAL 3.4 2.0 - - - -
9063 LEU* 4.2 23.2 - - + +
9253 VAL* 4.6 5.5 - - - +
9263 TYR* 1.3 77.7 + - - +
9283 TYR* 1.3 69.2 + - - +
9393 PHE* 3.7 1.1 - - - -
9403 LEU* 2.7 54.4 + - + -
9413 HIS* 3.0 39.4 + - + -
9723 LEU* 5.2 5.1 - - + +
9773 LEU* 5.3 3.1 - - - +
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Residues in contact with TYR 928 (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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8663 ILE* 4.4 6.1 - - + -
8803 VAL* 4.0 19.5 - - + +
8823 LEU* 3.5 27.4 - - - +
9043 TYR* 3.2 6.8 - - - +
9053 VAL* 2.5 68.4 + - + +
9073 VAL* 4.2 12.3 - - + -
9263 TYR* 3.6 30.6 - - + +
9273 THR* 1.3 78.6 - - - +
9293 LYS* 1.3 61.3 + - - +
9303 LEU 3.4 0.2 - - - -
9373 LEU* 4.1 20.9 - - + -
9383 GLU 3.2 29.2 - - - +
9393 PHE* 3.5 30.2 - + + -
9403 LEU 4.6 0.2 - - - +
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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