Contacts of the strand formed by residues 297 - 302 (chain A) in PDB entry 4PC0
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 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A HIS* 3.4 14.9 + - - -
292A GLY* 3.7 1.0 - - - -
293A SER 3.3 23.7 + - - -
295A ASP* 2.7 35.0 + - - +
296A LYS* 1.3 85.0 - - + +
298A VAL* 1.3 59.4 + - - +
299A ALA* 5.1 0.3 - - - +
309A LYS* 4.9 3.3 + - - -
312A SER* 3.6 25.3 + - - +
313A PHE 3.5 5.4 - - - -
314A GLU* 4.0 18.2 - - + +
320A ILE* 3.5 8.1 - - - +
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Residues in contact with VAL 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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290A ALA* 4.0 24.0 - - + -
291A THR 3.2 13.2 - - - +
292A GLY* 4.6 4.7 - - - -
297A THR* 1.3 77.2 - - - +
299A ALA* 1.3 59.3 + - - +
312A SER* 3.5 1.6 - - - -
313A PHE* 2.8 57.6 + - + +
316A HIS* 5.0 0.9 - - + -
320A ILE* 3.9 12.3 - - + +
323A VAL* 4.1 11.2 - - + -
333A LEU* 4.2 6.1 - - + -
335A SER* 3.8 31.2 - - - +
345A TRP* 4.4 6.7 - - + +
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Residues in contact with ALA 299 (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 HIS* 3.6 23.4 - - + +
290A ALA* 3.3 8.7 - - - +
291A THR* 2.8 29.5 + - - +
297A THR* 5.1 0.7 - - - +
298A VAL* 1.3 75.5 - - - +
300A LEU* 1.3 60.8 + - - +
301A TRP* 3.6 18.5 - - - +
309A LYS* 3.6 27.6 - - + +
311A HIS 3.4 5.4 - - - -
312A SER* 4.6 0.9 - - - +
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Residues in contact with LEU 300 (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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288A ILE* 4.1 16.6 - - + -
289A LEU 3.7 6.1 - - - +
290A ALA* 4.5 3.6 - - + -
299A ALA* 1.3 74.3 - - - +
301A TRP* 1.3 70.0 + - - +
309A LYS* 3.8 1.2 - - - +
310A LEU* 2.9 43.7 + - + -
311A HIS* 3.0 29.8 + - + +
313A PHE* 3.9 23.1 - - + -
325A TRP* 3.7 33.4 - - + -
333A LEU* 5.1 0.2 - - + -
347A LEU* 4.3 17.3 - - + -
350A ILE* 5.7 2.5 - - + -
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Residues in contact with TRP 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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252A LEU* 4.0 17.7 - - + -
269A VAL* 3.7 12.1 - - + -
270A ASP 4.4 2.7 - - - -
271A ALA* 3.4 43.1 - - + -
287A PHE 3.5 0.5 - - - +
288A ILE* 3.4 10.7 - - - +
289A LEU* 2.9 53.9 + - + -
291A THR* 3.1 29.4 + - + +
299A ALA* 3.6 13.5 - - + +
300A LEU* 1.3 77.7 - - - +
302A ASP* 1.3 58.7 + - - +
306A LEU* 3.6 39.3 - - + -
307A LYS 5.2 0.9 - - - -
308A LEU 4.1 3.4 - - - -
309A LYS* 3.6 45.8 - - + -
310A LEU* 3.8 7.2 - - - +
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Residues in contact with ASP 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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287A PHE* 3.3 9.4 - - - +
288A ILE* 4.7 6.1 - - + +
301A TRP* 1.3 72.1 - - - +
303A LEU* 1.3 65.0 + - - +
304A ARG* 2.8 67.0 + - - +
305A ASN* 3.1 31.5 + - + +
306A LEU* 3.5 8.5 - - - +
308A LEU 5.0 0.8 + - - -
310A LEU* 3.8 27.1 - - + +
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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