Contacts of the strand formed by residues 323 - 328 (chain A) in PDB entry 2PDA
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 VAL 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A GLU 3.2 7.8 + - - +
271A ARG* 3.6 5.3 - - + -
272A VAL 3.3 20.1 + - - -
321A ALA* 3.6 1.5 - - - +
322A LYS* 1.3 86.6 + - + +
324A ILE* 1.3 69.2 + - - +
356A PRO* 2.9 7.4 - - - +
357A LYS* 3.9 14.8 - - + +
359A LEU* 4.2 15.0 - - + -
382A MET* 3.3 47.3 - - + +
386A LYS* 4.1 15.5 - - + -
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Residues in contact with ILE 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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272A VAL* 3.3 21.8 - - + +
274A VAL* 3.1 36.8 - - + -
300A ILE* 5.5 1.1 - - + -
313A PHE* 4.5 11.9 - - + -
317A LEU* 5.3 3.8 - - + -
321A ALA* 4.7 8.1 - - + -
323A VAL* 1.3 81.0 - - - +
325A THR* 1.3 64.1 + - - +
326A VAL* 4.5 9.6 - - + -
344A VAL* 4.6 3.6 - - + -
348A PHE* 4.3 10.1 - - + -
356A PRO* 3.4 28.0 - - + -
357A LYS 3.0 7.8 + - - +
358A ILE* 3.2 13.0 - - + +
359A LEU 2.9 21.5 + - - +
382A MET* 4.1 0.4 - - - -
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Residues in contact with THR 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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272A VAL 3.2 5.1 + - - -
273A ILE* 3.4 8.3 - - - +
274A VAL 3.1 20.6 + - - -
324A ILE* 1.3 73.3 - - - +
326A VAL* 1.3 60.9 + - - +
327A LEU* 3.1 25.3 + - - +
359A LEU* 3.0 24.7 - - + -
361A GLY 4.7 0.2 + - - -
378A VAL* 3.7 11.8 - - + +
381A ASN* 5.4 0.4 - - - +
382A MET* 2.9 47.1 - - + -
390A PHE* 4.1 8.5 - - + -
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Residues in contact with VAL 326 (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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274A VAL* 3.6 12.3 - - + +
324A ILE* 4.5 3.6 - - + -
325A THR* 1.3 71.7 - - - +
327A LEU* 1.3 61.9 + - - +
328A ASP* 3.7 4.0 + - - +
340A LEU* 3.3 39.3 - - + +
341A TYR* 3.4 25.4 - - + +
344A VAL* 3.8 24.5 - - + -
358A ILE* 3.8 26.0 - - + -
359A LEU 2.9 7.2 + - - +
360A ALA* 3.8 2.6 - - - +
361A GLY 3.1 21.7 + - - +
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Residues in contact with LEU 327 (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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273A ILE* 4.1 16.8 - - + -
274A VAL 2.9 16.4 + - - +
275A SER* 4.2 11.9 - - - +
276A MET* 4.7 1.6 + - - +
325A THR* 3.1 30.3 + - - +
326A VAL* 1.3 74.0 - - - +
328A ASP* 1.3 60.2 + - - +
340A LEU* 3.6 18.9 - - - +
361A GLY* 3.3 17.7 - - - +
363A TYR* 3.7 26.1 + - + -
370A PHE* 3.5 35.7 - - + -
378A VAL* 4.0 21.1 - - + -
390A PHE* 4.1 4.5 - - + -
392A VAL* 5.4 0.7 - - + -
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Residues in contact with ASP 328 (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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131A TYR* 2.8 34.4 + - - -
326A VAL* 4.4 1.9 - - - +
327A LEU* 1.3 73.3 - - - +
329A ARG* 1.3 57.3 + - - +
330A THR* 3.2 9.0 + - + -
338A ASP* 3.2 37.8 - - + +
339A PRO* 3.7 2.1 - - - +
340A LEU* 3.3 15.1 + - - +
341A TYR* 3.2 29.1 + - - +
361A GLY 2.9 10.1 + - - +
362A ARG* 3.4 6.8 - - - +
363A TYR* 3.3 22.6 + - - -
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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