Contacts of the strand formed by residues 357 - 363 (chain C) in PDB entry 4UQJ
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 THR 357 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246C GLN 4.8 0.5 - - - +
247C ILE* 3.3 21.6 - - - +
342C SER 5.2 3.3 + - - +
343C GLY* 5.8 5.7 - - - -
344C ASN 5.7 2.4 - - - +
355C ASN 5.3 0.7 + - - -
356C TYR* 1.3 79.4 + - - +
358C ILE* 1.3 65.8 + - - +
359C ASN* 3.6 20.0 + - - +
373C TYR* 3.6 31.6 - - + -
374C TRP 3.7 3.4 - - - -
375C SER* 5.2 2.3 - - - -
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Residues in contact with ILE 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C PRO* 4.6 4.0 - - + -
116C ASP 4.1 9.6 - - - +
117C LEU* 4.2 1.8 - - + -
120C ALA* 4.1 17.3 - - + -
225C LEU* 4.0 22.9 - - + -
245C PHE* 3.7 37.7 - - + -
246C GLN 4.0 9.0 - - - +
247C ILE* 4.0 9.6 - - + -
356C TYR* 3.6 31.2 - - + -
357C THR* 1.3 77.1 - - - +
359C ASN* 1.3 65.3 + - - +
360C ILE* 3.3 6.1 - - - +
373C TYR* 4.2 0.2 - - - -
374C TRP* 2.8 40.6 + - + +
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Residues in contact with ASN 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C PHE* 3.5 4.2 - - - -
246C GLN* 2.9 51.7 + - + +
247C ILE 6.4 0.2 - - - -
249C ASP* 3.5 37.5 + - - +
357C THR* 3.6 21.7 - - - +
358C ILE* 1.3 69.7 - - - +
360C ILE* 1.3 62.2 + - - +
361C MET* 3.7 10.2 + - - +
370C LYS* 4.5 13.4 - - + +
372C GLY 3.5 10.8 - - - +
373C TYR* 4.0 5.1 - - - +
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Residues in contact with ILE 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LEU* 3.8 21.1 - - + -
128C TYR* 4.9 1.3 - - - +
244C GLY 3.7 6.7 - - - +
245C PHE* 4.4 17.0 - - + +
358C ILE 3.3 17.3 - - - +
359C ASN* 1.3 71.9 - - - +
361C MET* 1.3 65.8 + - - +
370C LYS* 3.6 4.0 - - - -
371C ILE* 3.0 54.2 + - + +
372C GLY* 2.8 15.8 + - - +
373C TYR* 3.5 21.8 - - - +
374C TRP* 3.6 12.6 - - + -
380C MET* 3.6 26.7 - - + -
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Residues in contact with MET 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C PHE* 3.3 25.8 - - + -
228C THR* 4.2 11.9 - - + -
243C SER* 3.2 8.2 - - - -
244C GLY 3.0 30.6 + - - +
246C GLN* 3.6 35.2 - - + +
359C ASN* 3.8 8.1 - - - +
360C ILE* 1.3 78.6 - - - +
362C GLU* 1.3 63.4 + - - +
368C PRO* 3.9 15.3 - - + -
369C ARG* 3.7 24.7 - - - +
370C LYS* 3.7 27.8 - - + +
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Residues in contact with GLU 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C TYR* 4.7 2.3 + - - -
128C TYR* 2.7 38.7 + - - +
219C HIS* 6.0 0.2 - - - -
227C PHE* 4.4 3.8 - - - -
241C GLU* 5.5 5.1 - - - +
242C VAL 3.5 5.4 - - - +
243C SER* 3.7 5.8 - - - +
361C MET* 1.3 75.1 - - - +
363C LEU* 1.3 64.0 + - - +
364C LYS* 3.6 2.1 + - + +
368C PRO* 3.5 1.4 - - - +
369C ARG* 2.9 33.9 + - + +
371C ILE* 3.3 38.9 - - + +
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Residues in contact with LEU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C PHE* 4.1 7.2 - - + -
232C LEU* 3.6 21.8 - - + -
235C ILE* 3.4 35.4 - - + +
236C GLN* 3.6 41.1 - - + +
240C ALA 5.4 1.6 - - - +
241C GLU* 5.3 3.1 - - - +
242C VAL* 2.9 32.5 + - + +
362C GLU* 1.3 71.1 - - - +
364C LYS* 1.3 59.6 + - - +
367C GLY 3.7 3.8 - - - -
368C PRO* 3.6 32.8 - - + -
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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