Contacts of the strand formed by residues 327 - 333 (chain D) in PDB entry 1SAE
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 327 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331B GLN* 3.4 37.0 - - - +
332B ILE 4.1 3.4 - - - -
333B ARG* 4.0 41.5 + - + +
322D PRO* 2.4 48.6 + - + +
323D LEU* 4.9 3.1 - - + -
324D ASP 4.4 1.1 + - - -
325D GLY 3.2 16.4 - - - -
326D GLU* 1.3 73.3 - - - +
328D PHE* 1.3 76.5 + - - +
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Residues in contact with PHE 328 (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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331B GLN* 3.1 20.6 - - - +
332B ILE 3.2 15.5 + - - +
334B GLY 3.4 14.6 - - - -
335B ARG* 3.3 44.9 - - + -
338B PHE* 3.5 33.7 - + + -
326D GLU* 3.1 44.4 - - + -
327D TYR* 1.3 80.3 - - - +
329D THR* 1.3 75.8 + - - +
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Residues in contact with THR 329 (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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329B THR* 5.7 5.8 - - - -
330B LEU 3.3 10.5 - - - -
331B GLN* 4.5 14.1 - - + +
332B ILE* 4.7 0.4 - - - +
338B PHE* 3.3 16.9 - - - -
328D PHE* 1.3 88.4 - - - +
330D LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 330 (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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329B THR* 3.3 4.6 - - - -
330B LEU* 3.0 31.4 + - + +
332B ILE* 3.9 26.7 - - + -
338B PHE* 4.1 11.4 - - + -
341B PHE* 4.3 4.3 - - + +
342B ARG* 4.1 42.4 - - + +
345B ASN* 4.2 20.2 - - + +
329D THR* 1.3 76.4 - - - +
331D GLN* 1.3 78.5 + - - +
332D ILE* 3.6 15.7 + - + +
341D PHE* 5.1 3.6 - - + -
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Residues in contact with GLN 331 (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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327B TYR* 3.5 40.8 - - + +
328B PHE 3.1 19.5 - - - +
329B THR* 4.3 8.6 - - + +
345B ASN* 2.9 22.0 + - - -
330D LEU* 1.3 79.1 - - - +
332D ILE* 1.3 61.1 + - - +
333D ARG 4.1 0.8 + - - +
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Residues in contact with ILE 332 (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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328B PHE* 3.2 34.7 + - - -
330B LEU* 3.9 27.4 - - + +
345B ASN* 4.3 9.0 - - - +
330D LEU* 3.8 18.8 - - + +
331D GLN* 1.3 78.6 - - - +
333D ARG* 1.3 72.0 + - - +
334D GLY 3.8 0.2 - - - +
337D ARG* 4.3 17.0 - - + +
338D PHE* 4.1 34.8 - - + +
341D PHE* 3.6 35.9 - - + -
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Residues in contact with ARG 333 (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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322B PRO* 5.7 1.2 - - - +
324B ASP* 2.8 42.7 + - - +
325B GLY* 3.9 17.6 - - - +
326B GLU 4.2 3.8 - - - -
327B TYR* 4.0 39.8 + - + -
345B ASN* 4.9 5.0 + - - +
349B GLU* 6.0 5.8 - - + -
331D GLN* 4.1 2.0 + - - +
332D ILE* 1.3 75.1 - - - +
334D GLY* 1.3 69.1 + - - +
337D ARG* 3.6 34.8 + - - +
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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