Contacts of the strand formed by residues 320 - 325 (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 ALA 320 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A SER* 3.9 5.0 - - - -
218A PRO* 3.1 24.9 - - + +
220A ILE* 5.5 3.3 - - + +
296A THR* 4.2 8.1 - - + -
319A GLN* 1.3 75.8 - - - +
321A LYS* 1.3 64.4 + - - +
322A ARG 3.4 0.9 - - - +
323A VAL* 4.3 16.2 - - + -
332A ILE* 3.8 17.7 - - + -
334A ASP 2.9 19.3 - - - +
335A GLY* 3.6 6.1 - - - -
336A VAL* 4.5 3.6 - - - +
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Residues in contact with LYS 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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215A LEU 4.4 0.2 - - - +
216A GLU* 4.5 2.1 - - - +
217A SER* 3.8 15.1 + - - -
320A ALA* 1.3 74.2 - - - +
322A ARG* 1.3 64.0 + - + +
333A ILE* 5.2 2.7 - - + -
334A ASP* 2.8 49.1 + - + +
335A GLY* 4.3 0.8 - - - -
336A VAL* 5.2 13.8 - - + +
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Residues in contact with ARG 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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214A GLU* 4.1 29.3 + - + -
215A LEU 3.6 18.4 - - - +
216A GLU* 5.1 15.7 + - + +
218A PRO* 4.9 0.7 - - - -
320A ALA* 4.4 0.7 - - - -
321A LYS* 1.3 83.3 - - + +
323A VAL* 1.3 85.7 + - - +
324A VAL* 4.3 9.1 - - - +
332A ILE* 3.7 4.3 - - - +
333A ILE* 3.0 55.5 + - + +
334A ASP 4.1 1.2 + - - +
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Residues in contact with VAL 323 (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 VAL 3.3 4.7 - - - +
214A GLU* 3.4 2.8 - - - -
215A LEU* 3.2 56.6 + - + +
218A PRO* 4.1 19.5 - - + -
220A ILE* 5.4 4.7 - - + -
248A LEU* 5.1 12.1 - - + -
320A ALA* 4.3 7.4 - - + -
322A ARG* 1.3 84.3 - - - +
324A VAL* 1.3 65.1 + - - +
325A ILE* 4.1 8.1 - - + -
330A THR* 5.8 1.6 - - + -
331A THR 3.2 7.4 - - - +
332A ILE* 4.0 22.4 - - + -
333A ILE 4.8 0.2 - - - +
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Residues in contact with VAL 324 (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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212A ALA* 4.6 14.4 - - + -
213A VAL 3.1 6.5 - - - +
214A GLU* 4.3 14.1 - - + +
322A ARG* 4.3 9.6 - - - +
323A VAL* 1.3 78.3 - - - +
325A ILE* 1.3 70.3 + - - +
326A ASN* 5.0 7.7 + - + +
329A THR 4.3 0.3 - - - +
330A THR* 3.4 1.6 - - - -
331A THR* 2.6 51.3 + - - +
333A ILE* 4.1 26.2 - - + -
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Residues in contact with ILE 325 (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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199A TYR* 3.5 16.4 - - + +
211A GLY 3.3 1.9 - - - +
212A ALA* 3.2 4.4 - - - -
213A VAL* 2.6 70.5 + - + +
215A LEU* 4.6 2.7 - - + -
248A LEU* 4.6 12.1 - - + -
274A ALA* 5.7 0.9 - - + -
276A VAL* 3.1 34.5 - - + -
323A VAL* 4.0 19.1 - - + +
324A VAL* 1.3 81.0 - - - +
326A ASN* 1.3 67.3 + - - +
329A THR 3.8 1.8 - - - -
330A THR* 3.3 30.7 - - + +
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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