Contacts of the strand formed by residues 370 - 375 (chain A) in PDB entry 5H1Y
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 GLN 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A ILE* 3.0 33.9 + - - +
218A GLY* 3.1 27.7 - - - +
219A ARG 2.8 26.5 + - - +
220A ASP* 3.4 5.2 - - - +
242A PHE* 3.6 22.2 - - - -
339A ARG 2.8 14.7 + - - +
340A TYR* 3.4 15.9 - - + -
341A LEU* 2.9 26.5 + - - +
369A ARG* 1.3 73.7 - - - +
371A THR* 1.3 60.7 + - - +
372A LEU* 4.1 7.4 - - + +
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Residues in contact with THR 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ASP* 2.7 45.1 + - - +
221A MET 3.2 3.6 + - - +
341A LEU* 3.3 21.8 - - + +
343A LEU* 4.8 9.0 - - + -
362A PHE* 4.9 1.1 - - + -
369A ARG* 2.8 36.7 + - - +
370A GLN* 1.3 76.3 + - - +
372A LEU* 1.3 69.6 + - - +
389A ALA 4.1 7.9 + - - +
390A LEU* 3.4 28.7 - - + +
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ILE* 3.5 37.9 - - + -
219A ARG 3.9 8.1 - - - +
221A MET* 3.4 14.4 - - + +
235A PHE* 3.9 15.0 - - + -
340A TYR* 3.2 36.1 - - + +
341A LEU 2.8 12.1 + - - +
342A ALA* 4.1 4.3 - - + -
343A LEU* 2.6 36.6 + - - +
370A GLN* 4.1 12.1 - - + +
371A THR* 1.3 91.4 - - - +
373A LEU* 1.3 56.2 + - - +
374A PHE* 3.9 14.8 - - + -
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A MET 3.0 11.5 + - - +
222A ILE* 3.6 8.9 - - + -
223A GLY 2.8 27.5 + - - -
343A LEU* 3.5 11.7 - - + +
346A ALA* 3.7 22.2 - - + -
372A LEU* 1.3 73.0 - - - +
374A PHE* 1.3 66.0 + - - +
375A SER* 3.8 24.7 - - - -
378A MET* 4.2 10.3 - - + -
382A ILE* 4.2 12.1 - - + -
385A PHE* 4.1 26.9 - - + -
386A ALA* 4.2 18.4 - - + -
389A ALA* 5.4 0.2 - - + -
390A LEU* 4.4 16.1 - - + +
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Residues in contact with PHE 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ILE* 4.5 3.8 - - + -
221A MET* 3.6 37.7 - - + -
223A GLY* 3.4 12.8 - - - -
225A ALA* 4.9 2.9 - - + +
231A LYS* 3.8 40.2 - - + -
234A VAL* 4.0 19.3 - - + -
235A PHE* 3.9 27.1 - + + -
342A ALA* 5.4 0.4 - - + -
343A LEU 2.6 19.4 + - - +
344A ASP* 3.9 16.4 - - - +
345A GLU* 2.9 10.3 + - - -
346A ALA* 2.8 30.5 + - - +
372A LEU* 3.9 25.4 - - + -
373A LEU* 1.3 80.2 - - - +
375A SER* 1.3 54.9 + - - +
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Residues in contact with SER 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLY 3.1 8.7 + - - +
224A ILE* 3.2 6.1 - - - +
225A ALA 3.2 23.5 + - - -
231A LYS* 6.1 1.1 - - - +
345A GLU* 4.9 1.3 - - - +
347A ASP* 3.2 29.5 + - - +
373A LEU* 3.8 18.4 - - - -
374A PHE* 1.3 76.0 - - - +
376A ALA* 1.3 59.9 + - - +
377A THR 2.5 26.3 + - - -
378A MET* 4.1 7.2 - - - -
382A ILE* 3.8 5.2 - - - +
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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