Contacts of the strand formed by residues 347 - 352 (chain A) in PDB entry 3NSH
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 PHE 347 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU 3.8 8.5 - - - +
159A GLN* 4.1 6.6 - - - -
160A LEU 4.3 2.1 + - - -
304A ILE* 3.9 21.5 - - + -
305A THR 3.5 22.7 - - - -
306A ILE* 3.8 10.3 - - + -
310A GLN* 3.8 13.0 - - - -
343A ILE 2.9 28.9 - - - -
344A MET* 3.0 18.4 + - - +
345A GLU 3.2 2.7 - - - -
346A GLY* 1.3 83.4 + - - +
348A TYR* 1.3 61.5 + - - +
349A VAL* 3.9 14.3 + - + +
360A PHE* 4.5 7.9 - + + -
361A ALA 3.2 14.6 - - - +
362A VAL* 4.3 2.2 - - - -
363A SER* 3.5 7.4 - - - -
374A ALA* 4.4 8.7 - - + -
375A ALA* 3.7 13.5 - - - -
376A VAL* 3.5 26.7 - - + -
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Residues in contact with TYR 348 (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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157A SER* 2.8 35.9 + - - -
158A LEU 3.8 5.2 - - - -
159A GLN* 3.6 20.4 - - + -
181A ILE* 3.9 5.4 - - + +
185A ILE* 3.4 5.5 - - + -
186A ASP* 2.9 30.0 + - - -
189A LEU* 3.8 26.2 - - + +
190A TYR* 3.2 55.6 - + + -
194A LEU* 4.1 5.2 - - + +
347A PHE* 1.3 73.4 - - - +
349A VAL* 1.3 60.5 + - - +
350A VAL* 3.9 17.8 + - + -
359A GLY 3.4 1.6 - - - +
360A PHE* 3.4 4.9 - - - -
361A ALA* 2.8 36.1 + - + +
363A SER* 3.6 4.2 - - - -
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Residues in contact with VAL 349 (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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157A SER* 3.3 2.3 - - - -
158A LEU 3.0 36.7 + - - +
233A VAL* 4.5 3.4 - - + -
344A MET* 4.3 22.4 - - + +
347A PHE* 3.9 25.8 - - + +
348A TYR* 1.3 78.2 - - - +
350A VAL* 1.3 63.2 + - - +
351A PHE* 3.6 31.4 - - + -
358A ILE* 3.8 18.6 - - + -
359A GLY 3.2 3.8 - - - +
360A PHE* 4.0 22.0 - - + -
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Residues in contact with VAL 350 (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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155A LEU* 4.2 10.1 - - + -
156A PHE 4.0 8.1 - - - +
157A SER* 4.0 10.8 - - - -
185A ILE* 3.7 39.3 - - + -
194A LEU* 3.8 23.8 - - + -
196A TYR* 4.6 4.3 - - + +
348A TYR* 4.0 11.2 - - + -
349A VAL* 1.3 75.9 - - - +
351A PHE* 1.3 61.9 + - - +
352A ASP* 3.3 17.0 + - + +
358A ILE* 3.1 9.6 - - - +
359A GLY* 2.7 43.3 + - - +
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Residues in contact with PHE 351 (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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39A THR* 3.7 22.9 - - + -
155A LEU* 3.4 2.4 - - - -
156A PHE* 2.7 63.1 + + + +
158A LEU* 3.8 17.9 - - + -
199A ILE* 5.6 0.7 - - - -
205A TYR* 3.8 43.3 - + + -
233A VAL* 3.9 16.4 - - + -
344A MET* 3.7 18.4 - - + -
349A VAL* 3.6 31.6 - - + -
350A VAL* 1.3 69.9 - - - +
352A ASP* 1.3 60.2 + - - +
353A ARG* 2.9 13.5 + - - +
357A ARG 3.8 2.2 - - - -
358A ILE* 4.3 11.9 - - + -
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Residues in contact with ASP 352 (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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155A LEU* 3.7 29.3 - - + +
196A TYR* 4.3 5.6 + - + -
199A ILE* 4.8 0.4 - - - -
350A VAL* 3.3 8.7 + - + -
351A PHE* 1.3 72.0 - - - +
353A ARG* 1.3 60.5 + - - +
354A ALA* 3.6 8.5 + - - +
355A ARG* 3.1 25.8 + - - +
356A LYS 2.9 18.5 + - - -
357A ARG* 2.8 61.7 + - + +
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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
------------------------------------------------------------
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