Contacts of the strand formed by residues 319 - 322 (chain A) in PDB entry 4BC4
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 HIS 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A SER* 2.9 24.5 + - - +
168A TYR* 3.4 39.2 - + - -
170A ARG* 3.1 30.8 + - - -
171A PHE* 3.4 10.8 - + - -
318A GLY* 1.3 80.7 + - - -
320A ILE* 1.3 64.7 + - - +
321A PHE* 3.8 23.7 + + + -
332A ALA* 3.1 4.2 - - - -
333A LEU* 2.9 50.2 + - + +
335A CYS* 4.4 12.9 - - - +
382A ILE* 6.2 2.0 - - - +
426A LEU* 4.9 1.6 - - - +
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Residues in contact with ILE 320 (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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163A THR 3.8 6.2 - - - +
164A GLY* 2.9 36.0 + - - +
165A SER* 5.0 0.2 + - - -
217A SER 4.5 0.2 - - - +
224A ILE* 3.7 13.0 - - + +
309A LEU* 3.9 13.0 - - + -
312A PRO* 3.6 21.8 - - + -
313A MSE 3.6 18.4 - - - +
314A PRO* 3.6 32.3 - - + -
318A GLY 5.6 0.2 - - - -
319A HIS* 1.3 76.7 - - - +
321A PHE* 1.3 68.4 + - - +
330A TYR* 4.0 13.0 - - + -
331A MSE 3.3 10.5 - - - +
332A ALA* 4.1 11.0 - - + -
426A LEU* 4.3 11.9 - - + +
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Residues in contact with PHE 321 (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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98A GLN* 3.6 37.0 - - - -
99A HIS* 4.6 9.4 - + - -
165A SER* 5.0 0.4 - - - -
171A PHE* 4.4 4.7 - + - -
214A SER* 3.8 5.8 - - - +
217A SER* 3.5 33.7 - - - -
218A GLY* 4.1 9.6 - - - -
224A ILE* 4.9 0.9 - - - -
282A PRO* 4.3 5.8 - - + -
319A HIS* 3.8 27.4 - + + -
320A ILE* 1.3 80.7 - - - +
322A CYS* 1.3 69.3 + - - +
330A TYR* 3.3 9.6 - - - +
331A MSE 2.8 55.8 + - + +
333A LEU* 3.9 23.1 - - + -
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Residues in contact with CYS 322 (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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213A TYR* 3.6 30.5 - - + +
214A SER* 2.8 24.8 + - - -
217A SER* 3.1 19.8 + - - -
222A LEU* 4.1 2.7 - - - -
224A ILE* 3.4 36.0 - - - +
227A LYS* 3.8 22.9 - - + -
321A PHE* 1.3 74.5 - - - +
323A ASN* 1.3 62.6 + - - +
324A PRO* 3.8 0.9 - - - +
327A SER* 5.1 2.5 - - - +
329A HIS 3.8 7.9 - - - +
330A TYR* 4.0 3.6 - - - -
331A MSE 4.0 0.5 - - - +
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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