Contacts of the strand formed by residues 457 - 465 (chain S) in PDB entry 1O19
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 457 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166S MET* 3.6 42.8 - - + -
167S LEU* 4.9 15.6 + - + +
170S ARG* 3.9 52.4 + - + +
171S GLU 4.5 3.8 - - - +
172S ASN* 2.9 18.4 - - - +
253S HIS* 3.5 7.0 - - - +
254S PHE* 2.7 35.0 + - - +
255S GLY 3.8 19.5 - - - -
256S ALA 4.4 10.2 + - - -
455S ARG* 3.8 0.6 - - - +
456S GLN* 1.3 117.7 + - + +
458S PHE* 1.3 58.1 + - - +
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Residues in contact with PHE 458 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166S MET* 3.7 4.0 - - - +
172S ASN* 3.0 35.4 + - + +
173S GLN 3.2 28.3 + - - -
249S PHE* 4.7 6.1 - + - -
251S ARG* 3.7 40.8 - - + -
252S ILE 3.0 13.9 - - - +
253S HIS* 3.6 32.1 - + + +
457S TYR* 1.3 78.7 - - - +
459S ILE* 1.3 68.8 + - - +
460S GLY* 3.6 19.1 - - - -
663S ASN* 4.3 15.5 - - - -
666S SER* 5.0 4.0 - - - -
667S THR* 4.0 16.4 - - - -
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Residues in contact with ILE 459 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162S ALA* 4.6 0.9 - - + -
163S TYR* 4.3 14.1 - - + +
166S MET* 3.7 16.6 - - + -
173S GLN* 3.6 22.0 - - + -
175S ILE* 4.2 16.2 - - + -
196S PHE* 3.7 42.4 - - + -
250S ILE 3.5 2.3 - - - +
252S ILE* 2.7 29.6 + - + +
254S PHE* 3.3 29.6 - - + -
458S PHE* 1.3 81.4 - - - +
460S GLY* 1.3 61.6 + - - +
461S VAL* 3.7 8.5 + - + +
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Residues in contact with GLY 460 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173S GLN 3.0 14.8 + - - -
174S SER* 3.0 5.7 - - - -
175S ILE* 2.7 32.6 + - - +
249S PHE* 3.9 18.4 - - - -
250S ILE 3.3 8.7 - - - -
458S PHE* 3.6 11.1 - - - -
459S ILE* 1.3 73.5 - - - +
461S VAL* 1.3 59.1 + - - +
462S LEU 3.9 0.7 - - - -
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Residues in contact with VAL 461 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175S ILE* 3.7 14.4 - - + +
177S ILE* 4.0 17.9 - - + -
189S THR* 3.7 30.5 - - + +
192S VAL* 4.8 11.4 - - + -
193S ILE* 4.7 14.6 - - + -
196S PHE* 4.9 1.3 - - + -
248S MLY 3.7 2.3 - - - +
249S PHE* 3.5 5.0 - - - -
250S ILE* 3.1 34.8 + - + +
252S ILE* 4.6 12.1 - - + -
459S ILE* 4.1 19.5 - - + +
460S GLY* 1.3 77.4 - - - +
462S LEU* 1.3 59.8 + - - +
463S ASP* 3.9 0.5 + - - +
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Residues in contact with LEU 462 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174S SER* 6.3 0.2 - - - -
175S ILE 3.0 11.7 + - - +
176S LEU* 3.6 37.5 - - + -
177S ILE* 2.9 34.8 + - - +
178S THR* 5.7 2.5 - - - +
248S MLY 3.5 7.2 - - - +
249S PHE* 3.6 22.9 - - + -
268S TYR* 5.1 0.4 - - + -
460S GLY 3.9 0.2 - - - -
461S VAL* 1.3 74.6 - - - +
463S ASP* 1.3 60.3 + - - +
464S ILE* 3.3 40.8 - - + +
487S LEU* 4.6 19.5 - - + -
660S LEU* 4.3 15.7 - - + -
664S LEU* 4.7 6.3 - - + -
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Residues in contact with ASP 463 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177S ILE* 4.0 5.8 - - + -
185S LYS* 4.4 19.8 + - - +
186S THR* 3.8 15.6 + - - +
189S THR* 3.1 37.8 + - + +
244S SER* 4.7 8.1 + - - -
246S PHE 4.5 7.8 - - - +
247S GLY* 3.3 0.7 - - - -
248S MLY 2.4 62.4 + - + +
461S VAL 3.9 0.4 + - - +
462S LEU* 1.3 74.4 - - - +
464S ILE* 1.3 68.3 + - - +
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Residues in contact with ILE 464 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177S ILE 3.7 7.9 + - - +
178S THR* 3.5 15.8 + - - +
185S LYS* 3.8 15.4 - - - +
247S GLY* 4.2 12.1 - - - -
248S MLY 4.2 5.8 - - - +
268S TYR* 4.3 18.6 - - + -
269S LEU* 6.1 2.0 - - + -
462S LEU* 3.3 32.0 - - + +
463S ASP* 1.3 86.0 + - - +
465S ALA* 1.3 84.8 + - + +
480S ILE* 4.6 14.6 - - + -
483S THR* 4.4 25.1 - - + -
487S LEU* 5.2 5.2 - - + -
660S LEU* 4.5 6.7 - - + -
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Residues in contact with ALA 465 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178S THR* 4.2 2.0 + - - -
179S GLY 4.2 9.2 - - - +
181S SER 6.3 0.4 - - - +
185S LYS* 4.6 8.2 - - - +
247S GLY* 5.7 0.2 - - - -
464S ILE* 1.3 92.1 - - + +
466S GLY* 1.3 60.2 + - - +
468S GLU* 5.3 6.3 - - - +
480S ILE* 4.4 21.0 - - + +
484S ASN* 2.5 27.9 + - - +
487S LEU* 5.6 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