Contacts of the strand formed by residues 330 - 335 (chain A) in PDB entry 4PKO
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 THR 330 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A GLN* 3.6 0.3 - - - -
195A PHE* 3.0 63.1 + - + +
197A ARG 3.0 17.6 + - - -
248A LEU* 5.5 5.2 - - + -
276A VAL* 3.9 15.1 - - + +
323A VAL* 5.8 1.8 - - + -
324A VAL 3.4 3.1 - - - +
325A ILE* 3.3 40.1 - - + +
329A THR* 1.3 72.7 - - - +
331A THR* 1.3 70.2 + - - +
332A ILE* 6.0 1.3 - - + -
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Residues in contact with THR 331 (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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190A VAL* 4.0 17.3 - - + -
191A GLU 4.5 2.9 - - - +
193A MET 3.1 12.8 - - - +
194A GLN* 3.1 30.6 + - + +
195A PHE* 5.6 0.2 - - - -
323A VAL* 3.2 7.4 - - - +
324A VAL* 2.6 51.6 + - + +
326A ASN* 5.2 2.4 + - - -
329A THR* 3.5 4.5 - - - +
330A THR* 1.3 81.0 + - - +
332A ILE* 1.3 75.4 + - - +
333A ILE* 4.1 6.7 - - + +
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Residues in contact with ILE 332 (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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191A GLU 3.6 1.0 - - - +
192A GLY* 3.4 1.9 - - - -
193A MET* 2.4 67.7 + - + +
195A PHE* 5.3 11.0 - - + -
220A ILE* 4.9 7.4 - - + -
250A ILE* 6.1 0.4 - - + -
292A ILE* 4.5 20.9 - - + -
295A LEU* 4.7 8.5 - - + -
296A THR* 4.8 10.5 - - + -
320A ALA* 3.8 11.9 - - + -
322A ARG 3.7 4.3 - - - +
323A VAL* 4.0 12.8 - - + -
330A THR* 6.0 1.3 - - + -
331A THR* 1.3 79.0 - - - +
333A ILE* 1.3 63.0 + - - +
334A ASP* 3.2 31.2 + - - +
335A GLY 4.4 0.7 - - - +
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Residues in contact with ILE 333 (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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191A GLU* 3.1 49.3 - - + +
192A GLY* 4.2 4.6 - - - -
321A LYS* 5.6 2.0 - - + -
322A ARG* 3.0 54.0 + - + +
324A VAL* 4.1 19.5 - - + -
331A THR* 5.1 6.1 - - + -
332A ILE* 1.3 73.7 - - - +
334A ASP* 1.3 66.3 + - + +
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Residues in contact with ASP 334 (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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192A GLY* 5.4 2.9 - - - -
295A LEU* 4.6 0.7 - - - -
320A ALA* 2.9 11.6 - - - +
321A LYS* 2.8 66.5 + - + +
322A ARG 4.1 1.7 + - - -
332A ILE* 3.1 11.7 - - - +
333A ILE* 1.3 85.5 - - + +
335A GLY* 1.3 79.6 + - - +
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Residues in contact with GLY 335 (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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295A LEU* 3.5 28.3 - - - +
319A GLN 3.7 1.8 - - - -
320A ALA* 3.6 13.2 - - - -
321A LYS 4.3 0.4 - - - -
334A ASP* 1.3 91.0 + - - +
336A VAL* 1.3 64.6 + - - +
337A GLY 3.7 2.6 + - - -
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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