Contacts of the strand formed by residues 348 - 353 (chain A) in PDB entry 2X7Z
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 ILE 348 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A ILE* 3.8 38.1 - - + -
334A ALA 3.6 2.9 - - - +
335A GLY 3.5 23.6 - - - +
336A GLY* 3.6 15.0 - - - -
346A ASN 4.6 0.7 - - - +
347A SER* 1.3 72.4 - - - +
349A TYR* 1.3 62.9 + - - +
370A LYS* 3.3 8.2 - - - +
371A LEU* 2.8 47.6 + - + +
379A LEU* 3.8 24.7 + - + +
382A VAL* 4.4 6.3 - - + -
383A THR 4.6 1.6 - - - +
384A HIS* 4.7 1.1 - - - +
387A ALA* 3.6 26.7 - - + -
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Residues in contact with TYR 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ILE* 3.2 8.8 - - - +
334A ALA 3.0 34.0 + - - +
341A HIS* 3.5 39.3 - + + +
342A TRP* 4.5 1.4 - + - -
345A ASP* 2.4 38.1 + - - -
347A SER* 3.4 28.5 - - - -
348A ILE* 1.3 73.2 - - - +
350A VAL* 1.3 67.8 - - - +
351A THR* 3.6 2.8 + - + +
368A GLY* 3.5 22.7 - - - +
369A ASP 3.3 4.5 - - - +
370A LYS* 3.7 31.4 + - + -
1409A IMD 3.9 24.9 - + - -
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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
----------------------------------------------------------
331A PHE* 4.1 14.4 - - + -
332A SER 3.5 11.7 - - - +
333A ILE* 4.4 2.9 - - + -
349A TYR* 1.3 73.2 - - - +
351A THR* 1.3 62.4 + - - +
352A LYS 4.0 4.5 - - - +
353A ILE* 3.7 31.0 - - + -
365A LEU* 4.0 30.5 - - + -
366A GLN 3.8 15.9 - - - +
367A ILE* 3.6 3.7 - - - +
368A GLY* 2.7 29.5 + - - -
369A ASP* 2.8 20.6 + - + +
370A LYS 5.5 0.2 - - - -
371A LEU* 4.7 11.4 - - + -
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Residues in contact with THR 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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332A SER* 2.8 28.9 + - - -
333A ILE 3.9 4.0 + - - -
334A ALA* 3.5 34.4 - - + +
341A HIS* 4.1 17.3 - - + +
349A TYR* 3.9 3.8 - - + +
350A VAL* 1.3 78.6 - - - +
352A LYS* 1.3 73.7 + - - +
367A ILE* 3.7 21.4 - - - +
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Residues in contact with LYS 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A PHE* 3.1 8.1 - - - +
332A SER* 2.9 53.8 + - - +
350A VAL* 3.8 0.7 - - - +
351A THR* 1.3 90.9 + - - +
353A ILE* 1.3 66.0 + - - +
354A ILE* 4.1 9.9 - - + -
367A ILE* 4.0 6.5 - - - +
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Residues in contact with ILE 353 (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 GLY 3.7 4.5 - - - +
331A PHE* 4.0 2.7 - - + -
350A VAL* 3.7 27.1 - - + -
352A LYS* 1.3 74.1 - - - +
354A ILE* 1.3 63.1 + - - +
355A GLU 3.7 1.9 + - - -
359A ALA* 4.2 2.0 - - + +
360A HIS* 3.5 47.8 - - + +
365A LEU* 3.8 42.0 - - + +
366A GLN* 4.4 1.1 - - - +
367A ILE* 4.0 25.7 - - + +
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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
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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