Contacts of the strand formed by residues 375 - 379 (chain A) in PDB entry 4XJO
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 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A LEU* 3.9 11.6 - - - +
356A LEU* 3.9 20.6 - - - -
369A ARG 3.6 4.3 - - - -
370A VAL* 4.1 4.5 - - - -
374A ILE* 1.3 73.9 - - - +
376A VAL* 1.3 62.3 + - - +
407A TYR* 3.2 6.8 - - - +
408A ALA 2.9 34.1 + - - +
426A MET* 3.6 2.8 - - - +
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Residues in contact with VAL 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A MET* 3.9 25.1 - - + +
231A PHE* 4.1 17.7 - - + -
356A LEU* 4.0 3.1 - - - +
367A ASP 3.9 0.3 - - - +
368A VAL* 3.3 8.3 - - - +
369A ARG* 2.8 71.0 + - + +
374A ILE* 4.1 7.0 - - + -
375A GLY* 1.3 79.3 - - - +
377A ILE* 1.3 75.1 + - - +
378A GLU 4.2 0.4 - - - +
405A LEU* 4.0 13.0 - - + -
406A VAL 3.8 2.0 - - - -
407A TYR* 4.0 11.4 - - + -
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Residues in contact with ILE 377 (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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356A LEU* 3.8 26.7 - - + -
359A ALA* 3.9 20.4 - - + -
365A VAL* 3.7 37.2 - - + -
367A ASP 3.6 2.2 - - - -
368A VAL* 4.5 3.8 - - + +
376A VAL* 1.3 75.7 - - - +
378A GLU* 1.3 62.1 + - - +
379A CYS* 3.7 8.8 + - - -
405A LEU* 3.5 3.5 - - - -
406A VAL* 2.7 47.9 + - + +
426A MET* 3.6 36.6 - - + +
427A VAL 4.1 0.7 - - - +
430A ALA* 4.1 10.8 - - + -
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Residues in contact with GLU 378 (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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365A VAL* 3.6 3.5 - - - +
366A THR* 2.7 48.0 + - - +
367A ASP* 2.8 26.0 + - - +
369A ARG* 2.7 42.4 + - - +
376A VAL* 3.9 2.0 - - - +
377A ILE* 1.3 70.6 - - - +
379A CYS* 1.3 53.3 + - - +
404A ASN* 3.5 26.6 + - - +
405A LEU* 3.8 13.0 - - + -
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Residues in contact with CYS 379 (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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364A ALA 3.1 13.0 - - - +
365A VAL* 4.8 1.6 - - - -
366A THR* 3.5 8.1 + - - +
377A ILE* 4.2 18.8 - - - -
378A GLU* 1.3 76.7 - - - +
380A ASP* 1.3 59.1 + - - +
381A ARG 3.3 15.5 - - - +
383A VAL* 4.4 2.5 - - + -
404A ASN* 2.8 43.3 + - - +
406A VAL* 4.2 19.1 - - - -
430A ALA* 4.5 10.3 - - - -
433A VAL* 4.2 20.6 - - + -
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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