Contacts of the strand formed by residues 355 - 361 (chain A) in PDB entry 3HYW
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 ALA 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348A ILE* 3.7 10.8 - - + -
349A ALA 3.2 14.4 - - - +
350A ASP* 3.8 7.4 - - - -
351A PHE* 3.7 9.6 - - - -
354A ASP* 1.3 82.3 - - - +
356A GLY* 1.3 61.5 + - - +
374A MET* 3.3 4.9 - - - +
375A GLY 3.1 26.7 + - - +
378A ALA* 3.6 11.8 - - + +
379A HIS* 3.5 24.2 - - - +
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Residues in contact with GLY 356 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A LEU* 5.5 1.1 - - - -
347A CSS 3.6 1.4 - - - +
348A ILE* 3.2 7.5 - - - +
349A ALA 2.8 36.5 + - - -
351A PHE* 3.3 19.4 - - - -
355A ALA* 1.3 71.7 - - - +
357A PHE* 1.3 61.5 + - - -
358A PHE* 3.9 15.1 - - - -
373A LYS 3.5 6.5 - - - -
374A MET* 4.4 3.6 - - - -
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Residues in contact with PHE 357 (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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346A ILE* 3.4 33.2 - - + -
347A CSS 3.7 1.1 - - - -
348A ILE* 3.7 24.2 - - + -
355A ALA 3.9 1.0 + - - -
356A GLY* 1.3 71.2 - - - -
358A PHE* 1.3 63.3 + - - +
359A PHE* 3.8 24.9 - - + -
371A ILE* 4.0 25.8 - - + -
372A THR* 3.4 5.0 - - - -
373A LYS* 2.6 44.2 + - + +
377A TRP* 3.7 35.9 - + + -
378A ALA* 4.4 4.9 - - + -
381A PHE* 5.6 2.9 - + - -
411A LEU* 4.6 2.7 - - + -
600A LMT 4.2 32.3 - - + -
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Residues in contact with PHE 358 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A PHE* 4.1 24.5 - + - -
199A ILE* 4.0 23.6 - - + -
202A SER* 3.7 31.0 - - - -
205A LEU* 4.1 27.8 - - + -
206A VAL* 4.8 2.9 - - + -
345A ALA 3.8 0.8 - - - +
346A ILE* 3.5 4.9 - - - +
347A CSS 2.7 54.2 + - + +
349A ALA* 4.4 11.9 - - + -
351A PHE* 5.1 2.9 - + - -
356A GLY* 3.9 21.8 - - - -
357A PHE* 1.3 77.4 - - - +
359A PHE* 1.3 60.4 + - - +
371A ILE 3.4 2.9 - - - -
372A THR* 3.9 20.9 - - + -
800A PS9 4.4 12.3 - - - -
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Residues in contact with PHE 359 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A ILE* 3.6 3.9 - - - +
315A MET* 4.8 2.7 - - - -
344A SER* 4.4 10.1 - - - -
345A ALA 3.2 17.7 - - - -
346A ILE* 3.7 16.4 - - + -
357A PHE* 3.8 20.0 - - + -
358A PHE* 1.3 75.1 - - - +
360A ALA* 1.3 63.2 + - - +
361A ASP* 3.5 33.2 - - + -
369A ARG* 4.0 17.3 - - + -
370A VAL* 3.0 9.8 - - - +
371A ILE* 2.8 45.9 + - + +
411A LEU* 3.8 52.3 - - + -
413A VAL* 4.7 7.0 - - + -
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Residues in contact with ALA 360 (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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199A ILE* 4.2 21.1 - - + +
344A SER* 3.4 4.3 - - - -
345A ALA* 3.0 33.6 + - + +
358A PHE 4.4 0.2 - - - -
359A PHE* 1.3 75.2 - - - +
361A ASP* 1.3 60.0 + - - +
362A PRO 3.5 6.5 - - - +
363A VAL* 3.6 13.3 + - + -
367A ARG* 3.7 28.7 - - - +
369A ARG 3.8 4.0 - - - -
370A VAL* 4.1 0.7 - - - -
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Residues in contact with ASP 361 (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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342A ARG* 2.6 40.2 + - - +
344A SER* 3.4 15.9 - - - -
359A PHE* 3.5 27.6 - - + -
360A ALA* 1.3 73.9 - - - +
362A PRO* 1.4 56.4 + - - +
367A ARG* 3.6 1.2 - - - +
368A GLU* 2.7 32.1 + - - +
369A ARG* 2.9 35.1 + - + +
411A LEU 5.0 0.3 - - - +
412A LYS 4.6 9.0 - - - +
413A VAL* 5.2 5.1 - - - -
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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