Contacts of the strand formed by residues 340 - 347 (chain A) in PDB entry 4M5X
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 ARG 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A TYR* 3.5 28.7 - - - +
332A ILE 3.3 10.3 - - - +
333A GLN* 2.8 54.3 + - - +
338A ASP* 5.3 0.8 + - - +
339A TYR* 1.3 88.3 - - - +
341A SER* 1.3 63.9 + - - +
342A ASP* 2.9 39.4 + - - +
394A LYS* 4.7 11.5 - - - +
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Residues in contact with SER 341 (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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330A SER 3.7 1.4 - - - +
331A TYR* 3.2 5.5 - - - -
332A ILE* 2.8 45.4 + - - +
339A TYR* 4.1 20.6 - - - -
340A ARG* 1.3 73.7 - - - +
342A ASP* 1.3 61.7 + - - +
343A ARG* 2.4 42.8 + - - +
379A TYR* 4.4 9.0 + - - -
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Residues in contact with ASP 342 (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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329A VAL* 4.1 14.7 - - + +
330A SER 3.6 2.7 - - - -
331A TYR* 3.3 17.3 - - - +
340A ARG* 2.9 41.4 + - - +
341A SER* 1.3 71.7 + - - +
343A ARG* 1.3 77.5 + - - +
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Residues in contact with ARG 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A VAL* 3.1 11.0 - - - +
330A SER* 2.9 52.4 + - - +
339A TYR* 4.8 5.7 + - - -
341A SER* 2.4 32.6 + - - +
342A ASP* 1.3 108.5 + - - +
344A ARG* 1.3 69.2 + - - +
345A GLU* 5.5 2.0 - - + +
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Residues in contact with ARG 344 (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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325A ARG* 4.1 12.3 - - - +
327A LYS* 3.6 37.0 - - + +
328A MET 3.5 6.1 - - - +
329A VAL* 4.8 0.9 - - - +
343A ARG* 1.3 79.8 - - - +
345A GLU* 1.3 64.5 + - - +
346A ASP* 2.8 40.6 + - - +
396A LEU* 5.2 7.0 - - + -
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Residues in contact with GLU 345 (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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327A LYS* 3.6 1.0 - - - -
328A MET* 2.7 60.7 + - + +
330A SER* 3.6 23.8 + - - -
343A ARG* 4.7 4.6 - - + +
344A ARG* 1.3 75.1 - - - +
346A ASP* 1.3 73.6 + - - +
347A TYR* 6.0 0.7 - - + -
393A VAL* 5.3 3.6 - - - +
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Residues in contact with ASP 346 (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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325A ARG* 3.6 29.6 + - + -
326A GLY 3.4 3.8 - - - +
327A LYS* 3.4 13.2 - - - +
344A ARG* 2.8 44.7 + - - -
345A GLU* 1.3 86.9 - - - +
347A TYR* 1.3 62.1 + - - +
348A TYR* 4.9 5.7 - - + -
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Residues in contact with TYR 347 (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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325A ARG* 3.4 4.7 - - - -
326A GLY* 2.9 52.4 + - - -
327A LYS 3.5 14.1 - - - -
328A MET* 3.7 35.7 - - + -
345A GLU* 6.0 0.7 - - + -
346A ASP* 1.3 77.0 - - - +
348A TYR* 1.3 67.7 + - - +
349A ASP 3.7 24.9 - - - +
350A ILE* 3.9 18.6 - - + -
395A PHE* 3.6 7.3 - + - -
397A THR 2.6 20.6 + - - -
398A LEU* 3.4 23.0 - - - +
399A PRO* 4.0 15.9 - - + -
402A LEU* 4.7 1.8 - - + -
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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