Contacts of the strand formed by residues 357 - 363 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B GLN 5.0 0.5 - - - +
247B ILE* 3.5 19.8 - - - +
342B SER 5.2 2.3 - - - +
343B GLY* 5.8 6.6 - - - -
344B ASN 5.7 2.8 - - - +
355B ASN 5.3 0.2 + - - -
356B TYR* 1.3 79.9 + - - +
358B ILE* 1.3 65.1 + - - +
359B ASN* 3.6 21.1 + - - +
373B TYR* 3.7 33.2 - - + -
374B TRP 3.7 3.4 - - - -
375B SER* 5.2 2.6 - - - -
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Residues in contact with ILE 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B PRO* 4.5 4.3 - - + -
116B ASP 4.0 14.1 - - - +
117B LEU* 4.3 1.1 - - + -
120B ALA* 4.2 14.6 - - + -
225B LEU* 4.1 22.7 - - + -
245B PHE* 3.9 36.1 - - + -
246B GLN 4.2 9.4 - - - +
247B ILE* 4.1 10.1 - - + -
356B TYR* 3.6 30.7 - - + -
357B THR* 1.3 75.7 - - - +
359B ASN* 1.3 64.9 + - - +
360B ILE* 3.3 5.7 - - - +
373B TYR* 4.2 0.4 - - - -
374B TRP* 2.8 41.2 + - + +
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Residues in contact with ASN 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B PHE* 3.6 4.3 - - - -
246B GLN* 3.0 42.8 + - + +
249B ASP* 3.6 34.2 + - - +
357B THR* 3.6 21.7 - - - +
358B ILE* 1.3 71.8 - - - +
360B ILE* 1.3 62.5 + - - +
361B MET* 3.7 14.4 + - - +
370B LYS* 4.5 13.8 - - + +
372B GLY 3.5 11.0 + - - +
373B TYR* 4.0 5.2 - - - +
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Residues in contact with ILE 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA* 5.4 0.2 - - + -
124B LEU* 3.6 21.1 - - + -
128B TYR* 5.0 0.9 - - - +
244B GLY 3.9 5.6 - - - +
245B PHE* 4.3 16.2 - - + -
358B ILE 3.3 17.5 - - - +
359B ASN* 1.3 71.9 - - - +
361B MET* 1.3 66.7 + - - +
370B LYS* 3.6 4.0 - - - -
371B ILE* 3.0 55.0 + - + -
372B GLY* 2.8 15.7 + - - +
373B TYR* 3.5 21.3 - - - +
374B TRP* 3.6 12.8 - - + -
380B MET* 3.6 26.9 - - + -
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Residues in contact with MET 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B PHE* 3.6 22.0 - - + -
228B THR* 4.5 11.2 - - + -
243B SER* 3.2 8.0 - - - -
244B GLY 3.0 32.3 + - - +
246B GLN* 3.6 33.7 - - + +
359B ASN* 3.8 9.9 - - - +
360B ILE* 1.3 78.9 - - - +
362B GLU* 1.3 64.0 + - - +
368B PRO* 3.9 14.6 - - + -
369B ARG* 3.7 25.1 - - - +
370B LYS* 3.6 28.0 - - + +
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Residues in contact with GLU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B TYR* 4.3 3.3 + - - -
128B TYR* 2.6 42.5 + - - +
219B HIS* 6.0 0.2 - - - -
227B PHE* 4.5 3.1 - - - -
241B GLU* 5.6 3.8 - - - +
242B VAL 3.6 4.9 - - - +
243B SER* 3.6 5.4 - - - +
361B MET* 1.3 76.1 - - - +
363B LEU* 1.3 61.8 + - - +
364B LYS* 3.6 1.9 + - + +
368B PRO* 3.5 1.4 - - - +
369B ARG* 2.9 34.6 + - + +
371B ILE* 3.3 38.5 - - + +
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B PHE* 4.0 8.3 - - + -
232B LEU* 3.9 21.5 - - + -
235B ILE* 3.6 34.3 - - + +
236B GLN* 3.8 30.7 - - + +
241B GLU* 5.1 4.2 - - - +
242B VAL* 2.8 34.9 + - + +
362B GLU* 1.3 73.2 - - - +
364B LYS* 1.3 66.6 + - - +
367B GLY 3.7 3.8 - - - -
368B PRO* 3.6 32.1 - - + -
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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