Contacts of the strand formed by residues 353 - 361 (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 TYR 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A PHE* 3.6 15.2 - - - -
307A ALA* 3.6 15.4 - - + +
308A GLN* 3.1 44.7 + - - +
309A LEU* 3.6 33.3 - - + +
328A VAL* 3.6 22.9 - - + +
330A MET* 4.1 11.8 - - + +
344A PHE* 3.7 19.5 - - + -
345A THR 3.5 1.3 - - - -
346A SER* 3.5 25.8 - - - -
350A GLY 2.6 32.3 + - - -
351A ILE 3.4 6.7 - - - -
352A VAL* 1.3 82.4 - - - +
354A SER* 1.3 61.5 + - - +
355A LYS 4.4 0.2 + - - -
641A LEU* 5.9 0.4 - - - +
642A CYS 5.6 0.9 - - - +
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Residues in contact with SER 354 (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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344A PHE* 3.3 4.9 - - - -
345A THR* 2.9 43.8 + - - -
353A TYR* 1.3 77.3 - - - +
355A LYS* 1.3 70.7 + - - +
356A SER* 3.2 0.7 + - - -
641A LEU* 5.2 20.6 - - - +
642A CYS 6.0 0.4 - - - -
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Residues in contact with LYS 355 (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 THR* 3.8 22.2 - - + -
343A ILE 4.0 0.2 - - - -
344A PHE* 3.9 20.4 - - + -
353A TYR 4.3 0.2 - - - -
354A SER* 1.3 79.1 + - - +
356A SER* 1.3 61.7 + - - +
357A LEU 4.7 2.2 - - - +
358A ASP* 2.8 43.4 + - - +
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Residues in contact with SER 356 (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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343A ILE* 2.8 28.2 + - - +
345A THR* 4.1 16.1 - - - +
354A SER 3.2 2.8 + - - -
355A LYS* 1.3 75.8 - - - +
357A LEU* 1.3 58.2 + - - +
401A GLY* 2.6 32.1 + - - +
404A TRP* 2.7 35.5 + - - -
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Residues in contact with LEU 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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341A GLY 4.2 0.2 - - - +
342A THR* 3.3 10.5 - - - +
343A ILE* 2.9 49.0 + - + +
355A LYS* 3.9 1.9 - - - +
356A SER* 1.3 80.7 - - - +
358A ASP* 1.3 68.4 + - - +
360A HIS* 4.6 3.5 - - + +
383A THR* 3.1 36.1 - - + -
385A VAL* 3.8 25.6 - - + -
395A MET* 4.8 7.6 - - + -
404A TRP* 3.7 42.8 - - + +
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Residues in contact with ASP 358 (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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341A GLY 4.5 0.4 - - - -
342A THR* 3.8 9.5 + - - -
355A LYS* 2.8 41.2 + - - -
357A LEU* 1.3 75.4 - - - +
359A ARG* 1.3 81.2 + - + +
360A HIS 3.2 3.5 + - - -
385A VAL* 3.5 16.3 - - - +
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Residues in contact with ARG 359 (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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340A PHE* 3.3 56.3 - - + +
341A GLY 3.1 10.8 + - - -
342A THR* 4.8 0.8 + - - -
358A ASP* 1.3 83.7 + - + +
360A HIS* 1.3 62.0 + - - +
361A LEU 3.3 0.2 + - - -
385A VAL* 3.2 5.0 - - + -
386A LEU* 2.6 60.5 + - - +
387A SER* 2.7 26.1 + - - +
388A GLU* 3.5 40.2 + - - +
390A ASN* 4.5 3.4 + - - -
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Residues in contact with HIS 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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321A LEU* 3.6 18.6 - - + -
331A HIS* 3.0 24.8 + + - -
340A PHE* 3.2 0.6 - - - -
341A GLY 2.6 37.7 + - - +
343A ILE* 3.3 36.4 - - + +
357A LEU* 4.6 6.1 - - + +
358A ASP 3.2 2.7 - - - +
359A ARG* 1.3 72.9 - - - +
361A LEU* 1.3 68.1 + - - +
362A TYR* 3.0 2.3 + + - -
369A THR* 3.2 25.7 + - - -
371A PHE* 3.9 4.3 - - + +
383A THR* 2.4 35.2 + - + -
384A SER 3.2 13.7 - - - -
385A VAL* 4.2 1.6 - - - -
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Residues in contact with LEU 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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339A GLY 3.6 11.9 - - - +
340A PHE* 4.2 2.9 - - - -
359A ARG 3.3 3.6 + - - -
360A HIS* 1.3 73.8 + - - +
362A TYR* 1.3 59.9 + - - +
363A THR* 4.2 4.3 - - + -
368A GLU 4.2 7.6 - - - +
369A THR* 3.0 22.6 + - - -
370A ASP 4.4 2.1 + - - +
384A SER* 3.0 25.4 + - - +
386A LEU* 4.6 16.4 - - + +
392A ILE* 3.7 46.9 - - + -
433A TYR* 3.4 45.5 - - + -
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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