Contacts of the strand formed by residues 357 - 363 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246D GLN 5.0 0.3 - - - +
247D ILE* 3.5 20.3 - - - +
342D SER 5.2 1.9 - - - +
343D GLY* 5.8 6.7 - - - -
344D ASN 5.7 2.4 - - - +
355D ASN 5.3 0.5 + - - -
356D TYR* 1.3 80.8 + - - +
358D ILE* 1.3 65.7 + - - +
359D ASN* 3.6 20.4 + - - +
373D TYR* 3.7 32.8 - - + -
374D TRP 3.7 2.6 + - - -
375D SER* 5.2 2.1 - - - -
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Residues in contact with ILE 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D PRO* 4.5 4.3 - - + -
116D ASP 4.0 13.0 - - - +
117D LEU* 4.3 1.8 - - + -
120D ALA* 4.2 14.4 - - + -
225D LEU* 4.1 22.2 - - + -
245D PHE* 3.9 36.3 - - + -
246D GLN 4.2 9.4 - - - +
247D ILE* 4.1 9.4 - - + -
356D TYR* 3.6 31.2 - - + -
357D THR* 1.3 77.1 - - - +
359D ASN* 1.3 65.8 + - - +
360D ILE* 3.3 5.7 - - - +
373D TYR* 4.2 0.2 - - - -
374D TRP* 2.8 41.5 + - + +
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Residues in contact with ASN 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D PHE* 3.6 4.5 - - - -
246D GLN* 3.0 42.7 + - + +
249D ASP* 3.6 35.2 + - - +
357D THR* 3.6 22.2 + - - +
358D ILE* 1.3 72.3 - - - +
360D ILE* 1.3 61.6 + - - +
361D MET* 3.7 14.7 + - - +
370D LYS* 4.5 14.0 - - + +
372D GLY 3.5 10.1 - - - +
373D TYR* 4.0 4.4 - - - +
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Residues in contact with ILE 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ALA* 5.4 0.2 - - + -
124D LEU* 3.6 20.4 - - + -
128D TYR* 5.0 0.9 - - - +
244D GLY 3.9 5.6 - - - +
245D PHE* 4.3 16.6 - - + -
358D ILE 3.3 17.5 - - - +
359D ASN* 1.3 72.3 - - - +
361D MET* 1.3 67.0 + - - +
370D LYS* 3.6 3.8 - - - -
371D ILE* 3.0 55.4 + - + -
372D GLY* 2.8 15.2 + - - +
373D TYR 3.5 21.5 - - - +
374D TRP* 3.6 13.2 - - + -
380D MET* 3.6 25.8 - - + -
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Residues in contact with MET 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D PHE* 3.6 21.8 - - + -
228D THR* 4.5 10.3 - - + -
243D SER* 3.2 8.2 - - - -
244D GLY 3.0 32.7 + - - +
246D GLN* 3.6 34.3 - - + +
359D ASN* 3.8 9.9 - - - +
360D ILE* 1.3 79.2 - - - +
362D GLU* 1.3 62.0 + - - +
368D PRO* 3.9 14.8 - - + -
369D ARG* 3.7 24.7 - - - +
370D LYS* 3.7 27.4 - - + +
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Residues in contact with GLU 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D TYR* 4.3 3.1 + - - -
128D TYR* 2.6 42.5 + - - +
219D HIS* 6.0 0.2 - - - -
227D PHE* 4.5 2.9 - - - -
241D GLU* 5.9 3.4 - - - -
242D VAL 3.6 5.4 - - - +
243D SER* 3.6 5.2 - - - +
361D MET* 1.3 75.3 - - - +
363D LEU* 1.3 62.3 + - - +
364D LYS* 3.6 2.5 + - + +
368D PRO* 3.5 1.5 - - - +
369D ARG* 2.9 35.2 + - + +
371D ILE* 3.3 38.3 - - + +
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Residues in contact with LEU 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D PHE* 4.0 8.1 - - + -
232D LEU* 3.9 21.3 - - + -
235D ILE* 3.6 33.4 - - + +
236D GLN* 3.8 31.7 - - + +
241D GLU* 5.1 4.9 - - - +
242D VAL* 2.8 34.4 + - + +
362D GLU* 1.3 72.4 - - - +
364D LYS* 1.3 67.0 + - - +
367D GLY 3.7 2.9 - - - -
368D 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