Contacts of the strand formed by residues 340 - 346 (chain A) in PDB entry 4N7E
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 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 HIS* 4.4 1.8 - - - -
333A ASP* 3.4 7.2 + - - +
334A GLU* 3.2 34.9 + - + +
338A THR* 2.7 66.6 + - + -
339A GLY* 1.3 79.3 - - - +
341A GLY* 1.3 64.0 + - - +
359A ARG* 3.3 66.6 - - + +
360A HIS 3.2 15.7 - - - +
361A LEU* 4.2 2.0 - - - -
362A TYR 3.7 2.4 + - - +
386A LEU* 3.6 19.1 - - + -
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Residues in contact with GLY 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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331A HIS* 3.4 13.4 - - - -
332A VAL 3.1 15.5 - - - -
334A GLU* 3.9 7.6 - - - -
340A PHE* 1.3 78.3 - - - +
342A THR* 1.3 64.2 + - - -
359A ARG* 3.1 9.4 + - - -
360A HIS* 2.6 31.3 + - - -
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Residues in contact with THR 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A MET 3.7 0.5 - - - +
331A HIS* 3.5 2.3 - - - -
332A VAL* 2.8 34.1 + - - -
334A GLU* 3.4 15.9 + - - -
341A GLY* 1.3 76.3 + - - -
343A ILE* 1.3 64.9 + - - +
344A PHE* 3.6 28.4 - - + -
355A LYS* 3.8 33.3 - - + -
357A LEU 3.3 13.2 - - - +
358A ASP* 3.8 9.2 + - - +
359A ARG 4.8 0.9 + - - -
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Residues in contact with ILE 343 (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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321A LEU* 3.8 15.9 - - + -
329A PHE* 3.9 26.2 - - + -
330A MET 3.4 6.1 - - - +
331A HIS* 4.5 0.4 - - - +
342A THR* 1.3 74.0 - - - +
344A PHE* 1.3 67.3 + - - +
355A LYS 3.8 0.3 - - - -
356A SER* 2.8 37.3 + - - +
357A LEU* 2.9 32.8 + - + -
360A HIS* 3.3 51.6 - - + +
371A PHE* 3.9 13.9 - - + -
404A TRP* 4.6 4.0 - - + -
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Residues in contact with PHE 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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309A LEU* 3.6 17.7 - - + -
310A PRO* 3.9 24.0 - - + -
328A VAL 3.6 0.5 - - - +
329A PHE* 3.5 2.9 - - - -
330A MET* 2.6 44.6 + - - +
332A VAL* 4.0 21.8 - - + -
342A THR* 3.6 37.0 - - + -
343A ILE* 1.3 78.1 - - - +
345A THR* 1.3 62.3 + - - +
353A TYR* 3.7 26.2 - - + -
354A SER 3.3 8.3 - - - +
355A LYS* 3.9 29.6 - - + -
664A HIS* 4.6 12.6 - + - -
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Residues in contact with THR 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 MET* 3.7 16.6 - - + -
328A VAL 3.4 3.6 - - - -
329A PHE* 3.4 38.6 - - + -
344A PHE* 1.3 73.7 - - - +
346A SER* 1.3 63.7 + - - +
353A TYR* 3.5 2.2 - - - -
354A SER* 2.9 45.1 + - - -
356A SER* 4.1 16.0 - - - +
400A GLN 3.8 11.1 + - - +
401A GLY* 4.6 3.2 + - - -
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Residues in contact with SER 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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279A PHE* 4.6 0.3 - - - -
327A MET* 3.6 4.7 - - - +
328A VAL* 3.0 34.0 + - - +
345A THR* 1.3 79.1 + - - +
347A ASP* 1.3 72.2 + - - +
350A GLY* 3.8 11.4 - - - -
352A VAL 3.3 7.6 - - - -
353A TYR* 3.5 30.4 - - - -
641A LEU* 5.0 2.7 - - - +
686A PRO* 3.2 20.1 - - - +
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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