Contacts of the strand formed by residues 329 - 334 (chain A) in PDB entry 2PO5
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 ASN 329 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A PHE* 4.4 2.8 - - + -
252A LYS* 3.6 22.8 - - + +
255A GLU* 3.8 20.6 + - + +
256A VAL* 3.3 22.9 - - + -
257A VAL* 3.0 28.8 + - - +
327A ARG 3.5 1.7 - - - -
328A LYS* 1.3 79.8 + - - +
330A ILE* 1.3 60.5 + - - +
363A GLU* 3.1 23.3 + - - +
364A ASN* 3.1 42.7 + - - +
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Residues in contact with ILE 330 (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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248A PHE* 3.2 9.1 - - - -
257A VAL* 3.5 20.2 - - + +
259A LEU* 3.9 25.4 - - + -
319A ILE* 4.1 31.9 - - + +
322A LEU* 3.9 16.6 - - + -
323A CYS* 4.5 7.2 - - - -
327A ARG 4.0 13.7 - - - +
328A LYS 4.5 0.2 - - - -
329A ASN* 1.3 81.5 - - - +
331A LEU* 1.3 63.8 + - - +
332A LEU* 4.0 16.8 - - + -
362A VAL* 4.8 4.5 - - + -
364A ASN 2.9 8.5 + - - +
365A ILE* 3.2 14.4 - - + -
366A ARG 3.0 24.1 + - - +
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Residues in contact with LEU 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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241A ILE* 3.8 26.0 - - + +
244A GLU* 3.6 28.0 - - + -
245A LEU* 3.5 33.9 - - + +
248A PHE* 4.0 7.4 - - + -
256A VAL* 3.7 15.7 - - + +
257A VAL 3.0 8.5 + - - +
258A ILE* 3.5 12.3 - - + +
259A LEU 2.9 25.1 + - - +
330A ILE* 1.3 74.0 - - - +
332A LEU* 1.3 63.0 + - - +
333A VAL* 4.2 5.8 - - + -
366A ARG 3.4 12.8 - - - +
368A ALA* 3.8 12.1 - - - +
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Residues in contact with LEU 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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259A LEU* 3.5 35.4 - - + +
261A SER* 5.3 1.8 - - - -
315A THR* 4.4 9.6 - - + -
319A ILE* 4.0 17.7 - - + -
330A ILE* 4.1 4.3 - - + -
331A LEU* 1.3 73.1 - - - +
333A VAL* 1.3 62.6 + - - +
334A PRO* 4.2 1.1 - - - -
348A LEU* 4.1 31.9 - - + +
353A SER* 3.6 24.9 - - - +
365A ILE* 3.9 16.6 - - + -
366A ARG 2.8 15.7 + - - +
367A ARG* 3.3 12.3 - - + +
368A ALA 3.0 26.3 + - - -
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Residues in contact with VAL 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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237A PHE* 4.6 8.7 - - + -
241A ILE* 3.9 28.5 - - + -
258A ILE* 3.6 26.5 - - + -
259A LEU 2.9 10.5 + - - +
260A PHE* 3.6 27.1 - - + -
261A SER* 2.8 31.3 + - - +
331A LEU* 4.0 8.3 - - + +
332A LEU* 1.3 81.8 - - - +
334A PRO* 1.3 58.5 - - + +
335A ILE* 2.8 22.5 + - + +
348A LEU* 5.3 0.4 - - - -
368A ALA* 4.2 6.3 - - + -
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Residues in contact with PRO 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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237A PHE* 3.5 16.6 - - + -
261A SER 3.6 9.0 - - - +
302A GLN* 5.7 0.2 - - - +
332A LEU 4.3 0.2 - - - -
333A VAL* 1.3 82.7 - - + +
335A ILE* 1.3 61.9 + - - +
336A ALA 3.3 4.6 + - - -
337A PHE* 3.6 19.8 + - + +
344A THR* 3.7 24.9 - - + -
348A LEU* 4.4 9.4 - - + -
367A ARG* 4.0 20.6 - - + +
368A ALA* 3.9 25.6 - - + +
369A GLU 5.2 0.9 - - - +
370A SER* 4.2 13.7 - - - +
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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