Contacts of the strand formed by residues 303 - 308 (chain A) in PDB entry 3PU3
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 TYR 303 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PRO* 3.3 16.2 - - + +
100A SER 3.6 17.5 - - - -
101A ALA* 4.0 14.8 - - + -
103A ASP* 4.0 16.2 - - + -
104A VAL* 3.6 42.5 - - + +
268A PHE 3.5 0.9 - - - +
269A TYR* 3.2 5.7 - - - -
270A LEU* 2.7 57.1 + - + +
272A ARG* 4.9 13.3 + - + -
301A LYS* 3.5 40.5 - - + +
302A CYS* 1.3 73.6 - - - +
304A LYS* 1.3 60.4 + - - +
305A CYS 3.9 0.3 + - - -
319A TRP* 4.6 9.4 - + - -
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Residues in contact with LYS 304 (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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18A EDO 5.0 0.3 + - - -
42A EDO 3.2 47.2 + - - -
98A PHE* 3.7 25.8 - - + +
99A PRO 3.1 10.6 + - - +
100A SER* 4.0 4.3 + - - -
101A ALA* 3.2 19.3 + - - +
267A THR* 3.8 24.9 - - + -
268A PHE 3.5 3.4 - - - -
269A TYR* 4.3 5.6 - - + -
302A CYS 3.8 0.8 + - - -
303A TYR* 1.3 72.0 - - - +
305A CYS* 1.3 61.7 + - - +
306A ILE* 4.1 25.6 + - + +
152B TYR* 4.9 10.9 + - - -
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Residues in contact with CYS 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A EDO 3.8 19.3 - - - -
101A ALA* 3.6 14.6 - - + -
105A VAL* 4.5 8.5 - - - -
128A LEU* 5.1 5.8 - - - -
266A LYS 3.8 0.2 - - - +
267A THR* 3.6 1.0 - - - -
268A PHE* 2.8 41.9 + - + +
270A LEU* 3.8 17.7 - - + -
304A LYS* 1.3 74.9 - - - +
306A ILE* 1.3 65.5 + - - +
307A VAL* 3.6 17.7 + - - -
313A LEU* 4.5 17.3 - - - -
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Residues in contact with ILE 306 (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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18A EDO 5.3 2.1 + - - -
128A LEU* 5.0 5.2 - - - +
265A GLU* 3.5 26.7 - - + +
266A LYS 3.8 5.2 - - - +
267A THR* 3.8 20.4 - - + +
304A LYS* 4.1 29.8 + - + +
305A CYS* 1.3 76.9 - - - +
307A VAL* 1.3 65.7 + - - +
308A LYS* 3.9 24.0 + - + +
311A GLN* 3.9 6.1 - - - +
151B ASN* 3.2 35.4 - - + +
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.6 6.7 - - + -
259A TYR* 5.0 1.8 - - + +
261A VAL* 3.7 23.6 - - + +
265A GLU* 3.4 3.5 - - - -
266A LYS 2.8 35.5 + - - +
268A PHE* 3.7 29.8 - - + -
305A CYS* 4.2 10.3 - - - +
306A ILE* 1.3 74.6 - - - +
308A LYS* 1.3 62.5 + - - +
311A GLN* 3.7 29.8 - - + +
312A THR 4.6 0.7 - - - +
313A LEU* 4.1 24.9 - - + +
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Residues in contact with LYS 308 (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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261A VAL* 3.7 7.7 - - - +
264A GLY 3.8 1.6 - - - -
265A GLU* 4.0 27.9 + - + +
306A ILE* 3.9 21.3 - - + +
307A VAL* 1.3 77.5 - - - +
309A GLN* 1.3 70.3 + - + +
310A GLY 3.3 0.2 + - - -
311A GLN* 2.8 41.1 + - + +
150B GLU* 5.3 6.7 - - - +
151B ASN* 3.3 36.8 + - - +
155B PRO* 4.0 33.7 - - + +
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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