Contacts of the strand formed by residues 342 - 349 (chain A) in PDB entry 5I35
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 GLY 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A ALA* 4.0 2.4 - - - -
339A ALA* 3.1 28.8 + - - +
341A ILE* 1.3 78.2 - - - +
343A GLN* 1.4 63.0 + - - +
358A LYS* 5.8 0.2 - - - -
359A ILE 3.2 13.9 - - - -
360A GLN* 4.1 0.2 - - - -
361A TYR* 3.2 32.5 + - - -
408A TYR* 5.7 1.3 - - - -
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Residues in contact with GLN 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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306A PHE* 3.2 29.2 - - + +
307A MSE 3.5 32.1 + - - +
309A LEU* 5.8 0.7 - - - +
312A MSE 3.3 32.8 - - - +
335A PRO* 3.7 21.7 - - + +
337A ALA 3.6 7.0 - - - +
338A ALA* 4.6 0.2 - - - +
339A ALA* 4.3 1.7 - - - +
342A GLY* 1.4 76.8 - - - +
344A VAL* 1.3 64.3 + - - +
345A HIS* 2.9 30.7 + - - +
357A MSE 3.6 0.9 - - - +
358A LYS* 3.5 2.1 - - - +
359A ILE* 2.7 35.3 + - - +
361A TYR* 3.9 6.1 - - + +
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Residues in contact with VAL 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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335A PRO* 3.4 3.1 - - - +
336A PHE* 3.0 39.6 + - + -
337A ALA 2.8 18.0 + - - +
339A ALA* 4.4 4.0 - - + -
343A GLN* 1.3 79.6 - - - +
345A HIS* 1.3 64.1 + - - +
356A ALA* 3.8 28.0 - - + -
357A MSE 3.2 12.6 - - - +
358A LYS* 3.6 22.4 - - + +
700A ANP 3.6 39.5 - - + +
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Residues in contact with HIS 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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309A LEU* 4.9 2.9 - - + -
312A MSE 3.9 10.3 - - + +
331A PHE* 3.7 30.9 - + + -
332A GLU 2.9 22.1 + - - +
333A GLU 3.2 22.9 + - - -
335A PRO* 3.5 20.1 - - + +
336A PHE* 4.5 1.1 - - - +
343A GLN* 2.9 34.1 + - + -
344A VAL* 1.3 78.3 - - - +
346A LEU* 1.3 64.3 + - - +
347A ALA 3.8 0.2 + - - -
356A ALA* 3.6 1.9 - - - -
357A MSE 2.8 40.7 + - + +
359A ILE* 3.6 22.7 - - + -
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Residues in contact with LEU 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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330A TYR* 4.9 4.0 - - + -
331A PHE* 4.1 0.7 - - - -
332A GLU* 3.0 60.1 + - + +
334A ARG 5.4 0.4 + - - -
336A PHE* 3.1 46.3 - - + +
345A HIS* 1.3 76.1 - - - +
347A ALA* 1.3 62.4 + - - +
355A VAL 3.5 5.2 - - - +
356A ALA* 4.7 1.1 - - + -
447A LEU* 3.3 33.7 - - + -
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Residues in contact with ALA 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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328A LEU* 4.2 10.3 - - + -
330A TYR* 3.4 19.7 - - - +
331A PHE* 4.4 3.6 - - + -
345A HIS 3.8 0.2 + - - -
346A LEU* 1.3 77.3 - - - +
348A ARG* 1.3 61.8 + - - +
354A GLU* 3.6 6.1 - - - +
355A VAL* 3.0 44.2 + - + +
357A MSE 3.9 23.6 - - + -
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Residues in contact with ARG 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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328A LEU* 3.4 6.3 - - - -
329A GLU* 2.7 70.5 + - - +
330A TYR* 3.0 47.2 + - + +
347A ALA* 1.3 75.4 - - - +
349A MSE 1.3 62.1 + - - +
352A GLY* 3.4 38.1 - - - +
353A ARG 3.6 4.3 - - - +
354A GLU* 4.4 12.2 - - + +
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Residues in contact with MSE 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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327A LYS* 3.5 10.3 - - - +
328A LEU* 3.9 15.9 - - + +
329A GLU* 3.9 1.9 - - - -
348A ARG* 1.3 78.7 - - - +
350A LYS* 1.3 69.0 + - - +
351A GLY 3.3 2.5 - - - +
352A GLY* 2.7 18.4 + - - -
353A ARG* 2.8 65.2 + - + +
355A VAL* 4.1 18.8 - - + -
434A VAL* 3.8 24.9 - - + -
436A GLU* 4.8 6.5 - - - +
437A LEU* 4.0 9.0 - - + -
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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