Contacts of the strand formed by residues 297 - 302 (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 ILE 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A GLY* 3.9 2.3 - - - -
266A ALA* 3.2 22.5 + - - +
269A ALA* 3.3 5.8 - - - +
271A ARG* 3.2 32.5 - - - +
287A ILE* 4.1 22.0 - - + +
290A LEU* 3.4 44.4 - - + -
291A ALA* 5.0 2.3 - - + +
295A GLU* 3.3 18.1 + - + +
296A LYS* 1.3 78.1 - - - +
298A GLY* 1.3 59.4 + - - +
379A TYR* 3.6 34.8 - - + -
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Residues in contact with GLY 298 (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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263A TYR* 3.1 20.0 - - - -
264A VAL 3.4 7.6 - - - -
269A ALA* 3.5 1.6 - - - +
271A ARG 3.0 9.3 + - - -
272A VAL* 3.7 8.0 - - - -
273A ILE* 3.2 12.0 + - - +
287A ILE* 3.4 6.3 - - - -
297A ILE* 1.3 75.1 - - - +
299A LEU* 1.3 59.2 + - - -
379A TYR* 2.6 23.0 + - - -
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASP 3.5 0.3 - - - +
263A TYR* 3.1 11.6 - - - -
264A VAL* 2.8 42.0 + - + +
272A VAL* 4.1 0.4 - - - -
273A ILE* 3.1 32.1 - - + +
275A SER* 3.9 19.7 - - - +
280A CYS* 3.7 27.4 - - - +
283A ILE* 3.7 16.8 - - + -
284A GLU* 4.1 9.2 - - + +
287A ILE* 3.5 11.2 - - + -
298A GLY* 1.3 75.3 - - - +
300A ILE* 1.3 72.7 + - - +
301A LYS* 3.9 25.8 - - + +
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Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PHE* 3.9 35.7 - - + -
262A ASP 3.3 6.1 - - - +
263A TYR* 3.9 4.7 - - + -
272A VAL* 4.3 9.0 - - + -
273A ILE 2.8 9.0 + - - +
274A VAL* 3.5 12.6 - - + +
275A SER 3.1 24.8 + - - +
299A LEU* 1.3 75.8 - - - +
301A LYS* 1.3 63.3 + - - +
302A VAL 3.7 0.2 + - - -
313A PHE* 3.9 26.0 - - + +
316A ALA* 3.6 22.7 - - + +
317A LEU* 3.7 35.0 - - + +
324A ILE* 5.5 0.7 - - + -
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Residues in contact with LYS 301 (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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144A SER* 4.6 1.5 + - - +
148A GLU* 5.0 1.0 + - - -
261A PHE* 3.5 2.3 - - - -
262A ASP* 2.8 34.8 + - + +
264A VAL* 3.4 25.1 - - + -
280A CYS* 3.5 35.9 + - + +
281A GLU* 3.2 24.5 + - - -
284A GLU* 2.8 30.5 + - - -
299A LEU* 3.9 15.0 - - + -
300A ILE* 1.3 73.1 - - - +
302A VAL* 1.3 62.9 + - - +
303A ARG* 3.7 36.5 + - - +
476A GLN* 4.6 0.4 - - - +
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Residues in contact with VAL 302 (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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142A ALA* 4.4 6.4 - - - +
261A PHE* 3.6 30.3 - - + -
274A VAL* 3.8 23.8 - - + -
275A SER 3.0 19.5 + - - +
276A MET* 3.3 44.0 - - + +
277A GLY 4.9 1.0 + - - -
280A CYS* 5.6 0.3 - - - -
300A ILE 4.4 0.2 - - - +
301A LYS* 1.3 74.8 - - - +
303A ARG* 1.3 66.3 + - - +
305A TYR* 4.4 18.6 - - + -
340A LEU* 4.1 11.9 - - + -
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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