Contacts of the strand formed by residues 349 - 353 (chain A) in PDB entry 1XZQ
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 MET 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A LEU* 4.5 2.2 - - - -
323A VAL* 3.1 21.3 - - + +
325A ILE* 4.3 10.3 - - + -
336A GLU* 4.1 23.1 - - + +
339A ILE* 3.4 48.9 - - + -
340A LYS* 4.3 5.4 - - + -
343A LEU* 4.8 4.0 - - + -
345A THR 3.9 8.3 - - - +
346A ASP* 2.9 43.5 + - + +
347A ARG 3.4 3.2 + - - +
348A HIS* 1.3 81.2 - - - +
350A VAL* 1.3 61.0 + - - +
369A ARG* 5.4 3.0 + - - -
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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
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322A LEU* 4.1 13.0 - - + -
323A VAL 2.7 16.8 + - - +
324A VAL* 3.2 22.0 - - + +
325A ILE* 3.1 26.2 + - - +
349A MET* 1.3 74.7 - - - +
351A LYS* 1.3 65.4 + - - +
352A ILE* 4.4 7.6 - - + -
362A LYS* 3.9 26.5 - - + -
363A LEU* 5.3 0.4 - - + -
366A SER* 3.7 29.8 - - - +
369A ARG* 5.4 1.8 - - - +
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Residues in contact with LYS 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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325A ILE* 3.5 34.5 - - + +
327A LYS* 3.8 22.3 - - + +
332A GLU* 3.0 28.5 + - - +
336A GLU* 3.4 27.4 - - + +
350A VAL* 1.3 77.5 - - - +
352A ILE* 1.3 61.9 + - - +
353A SER* 3.8 10.1 + - - -
356A LYS* 6.1 1.4 - - - +
358A GLU* 3.8 2.8 - - - +
362A LYS* 3.0 22.5 + - - -
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Residues in contact with ILE 352 (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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227A LEU* 3.9 18.2 - - + -
324A VAL* 3.6 24.7 - - + -
325A ILE 3.2 8.9 + - - +
326A ASN* 3.3 8.8 + - - +
327A LYS* 3.1 22.3 + - - -
350A VAL* 4.1 8.2 + - + -
351A LYS* 1.3 72.8 - - - +
353A SER* 1.3 59.7 + - - +
358A GLU* 3.7 33.9 - - + +
359A GLY* 3.8 8.5 - - - +
362A LYS* 3.9 16.6 - - + -
363A LEU* 3.5 42.0 - - + +
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Residues in contact with SER 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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327A LYS* 3.6 27.6 + - - -
351A LYS* 3.8 10.4 + - - -
352A ILE* 1.3 74.4 - - - +
354A ALA* 1.3 62.5 + - - +
355A LEU* 3.3 17.5 + - - +
356A LYS* 3.4 22.8 + - - +
357A GLY 3.6 1.2 + - - -
358A GLU* 2.8 45.8 + - - +
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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