Contacts of the strand formed by residues 244 - 249 (chain A) in PDB entry 3PU8
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 SER 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A VAL* 3.8 13.7 - - - -
189A VAL* 3.9 11.7 - - - -
191A ASN* 3.3 23.2 + - - -
240A CYS* 3.6 2.8 - - - +
241A VAL* 3.0 24.3 + - - -
243A ASP* 1.3 79.4 - - - +
245A TYR* 1.3 63.9 + - - +
324A LEU* 3.3 8.9 - - - +
325A THR* 2.9 39.1 + - - -
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Residues in contact with TYR 245 (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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84A ASN* 4.1 6.1 - - + -
85A GLY* 4.0 3.8 - - - -
89A PHE* 3.3 42.2 - + - -
90A ILE* 3.6 16.4 - - + -
93A LEU* 3.9 19.5 - - + -
162A THR* 5.7 2.4 - - - +
164A VAL* 3.7 25.2 - - + +
167A GLN* 3.9 17.9 + - - +
191A ASN* 4.7 3.0 + - - +
244A SER* 1.3 81.1 + - - +
246A THR* 1.3 69.0 + - - +
247A ASP* 2.6 48.2 + - + -
248A PHE* 4.0 8.7 - - - -
269A TYR* 5.5 1.6 - + - -
294A PHE* 4.1 4.2 - + - -
322A ALA* 4.0 12.5 - - + +
323A THR* 3.3 23.1 - - - -
324A LEU* 4.7 0.9 - - - -
325A THR* 5.5 0.4 - - - -
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Residues in contact with THR 246 (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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2A OGA 3.5 26.1 + - - +
167A GLN* 5.7 0.7 - - - -
191A ASN* 4.7 4.5 + - - -
193A THR* 4.5 11.1 + - - +
245A TYR* 1.3 78.9 + - - +
247A ASP* 1.3 68.8 + - - +
249A HIS* 3.8 20.4 - - + +
322A ALA* 3.1 8.0 - - - +
323A THR* 2.9 42.5 + - - +
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Residues in contact with ASP 247 (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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84A ASN* 2.9 30.0 + - - +
167A GLN* 4.6 14.4 + - - +
245A TYR* 2.6 39.8 + - + -
246A THR* 1.3 81.1 - - - +
248A PHE* 1.3 80.2 + - - +
249A HIS* 2.9 24.4 + - - +
284A TRP* 3.6 18.7 - - + -
290A HIS* 4.6 4.3 - - + +
291A SER* 4.6 5.0 + - - -
293A MET 5.3 0.3 - - - +
294A PHE* 5.6 0.5 - - - -
295A PHE 5.4 0.3 + - - -
321A TYR 3.5 0.7 - - - +
322A ALA* 3.7 0.2 - - - -
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Residues in contact with PHE 248 (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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245A TYR* 4.0 1.3 - - - -
247A ASP* 1.3 91.0 + - - +
249A HIS* 1.3 61.3 + - - +
269A TYR* 3.7 24.5 - + + -
271A ILE* 3.7 22.4 - - + -
281A TYR* 3.9 1.8 + - - -
284A TRP* 3.3 31.8 - - + -
285A ARG* 4.9 3.3 + - - -
294A PHE* 3.9 24.2 - + - -
295A PHE* 3.6 21.3 - - + -
296A ALA* 3.7 31.6 - - + -
302A CYS* 4.0 8.1 - - - -
320A ILE* 4.0 11.2 - - + -
321A TYR* 3.2 13.7 - - - -
322A ALA* 3.5 22.7 - - + -
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Residues in contact with HIS 249 (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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2A OGA 3.2 12.5 + - - -
246A THR* 3.8 15.7 - - + +
247A ASP 2.9 21.8 + - - +
248A PHE* 1.3 77.0 - - - +
250A ILE* 1.3 70.6 + - - +
251A ASP* 3.2 12.1 + - - -
281A TYR* 3.4 16.7 - - - +
285A ARG* 6.0 2.2 - - - +
319A TRP 3.6 1.6 - - - +
320A ILE* 3.4 3.1 - - - +
321A TYR* 3.0 50.3 + + - +
322A ALA* 5.1 0.4 - - - -
323A THR* 5.9 0.2 - - + -
453A FE 2.2 31.4 - - - -
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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