Contacts of the strand formed by residues 309 - 314 (chain A) in PDB entry 3OOT
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 PHE 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A LYS* 5.9 0.9 - - - -
267A TYR* 3.7 49.8 - + + -
268A THR 4.1 9.4 - - - -
269A LEU* 4.2 11.9 - - + -
305A PHE* 3.0 42.9 + + + +
306A ILE* 3.1 17.0 - - - +
308A LYS* 1.3 99.5 - - + +
310A TYR* 1.3 55.9 + - - +
311A THR* 2.8 26.0 + - - -
322A PHE* 4.1 11.2 - - + -
323A ALA 3.3 18.8 - - - +
324A LEU* 3.9 18.8 - - + -
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Residues in contact with TYR 310 (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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152A SER* 3.3 32.9 - - - -
153A PHE 3.7 11.7 - - - -
154A TYR* 3.6 29.4 - + + +
164A GLN* 4.5 1.3 + - - -
166A VAL* 4.1 6.2 - - - +
170A SER* 3.5 13.0 - - - -
171A ASP* 2.8 33.9 + - + +
174A HIS* 3.6 31.0 - - + +
175A TYR* 3.7 20.9 - + + -
179A PHE* 3.6 21.1 - + - -
306A ILE 4.5 1.3 - - - -
309A PHE* 1.3 69.6 - - - +
311A THR* 1.3 59.5 + - - +
321A GLY 3.6 0.9 - - - +
322A PHE* 3.5 5.0 - - - -
323A ALA* 2.7 34.1 + - + +
325A ALA* 3.7 10.3 - - + +
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Residues in contact with THR 311 (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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151A PHE 4.2 0.2 - - - +
152A SER* 3.3 3.8 - - - -
153A PHE* 2.8 40.7 + - - +
214A VAL* 4.1 3.6 - - + -
306A ILE* 3.8 17.4 - - - +
309A PHE 2.8 15.8 + - - -
310A TYR* 1.3 73.9 - - - +
312A GLU* 1.3 62.1 + - - +
313A PHE* 3.6 33.1 - - + -
320A ILE* 3.7 13.2 - - + -
321A GLY 3.4 2.0 - - - -
322A PHE* 3.4 30.9 - - + -
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Residues in contact with GLU 312 (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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148A GLU* 5.3 3.8 - - - +
150A VAL* 4.3 30.3 - - + +
151A PHE 4.2 1.8 - - - +
152A SER* 3.3 18.6 - - - +
169A GLY* 4.6 0.3 - - - -
170A SER* 2.7 20.4 + - - -
179A PHE* 4.0 20.6 - - + -
181A TYR* 3.0 34.8 + - - -
310A TYR 4.2 0.2 + - - -
311A THR* 1.3 72.7 - - - +
313A PHE* 1.3 64.0 + - - +
314A ASP* 3.8 5.2 + - - +
320A ILE* 3.4 7.6 - - - +
321A GLY* 2.8 41.8 + - - +
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Residues in contact with PHE 313 (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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33A THR* 3.7 19.5 - - + -
150A VAL* 3.3 7.6 - - - +
151A PHE* 2.7 72.2 + + + +
153A PHE* 3.6 23.8 - + - -
190A TRP* 3.6 34.8 - + + -
214A VAL* 3.7 32.1 - - + -
216A THR* 3.8 10.1 - - + -
311A THR* 3.6 27.1 - - + -
312A GLU* 1.3 71.5 - - - +
314A ASP* 1.3 60.0 + - - +
315A ARG 3.7 1.5 + - - -
319A ARG 4.2 1.6 - - - -
320A ILE* 4.0 9.4 - - + -
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Residues in contact with ASP 314 (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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150A VAL* 3.6 21.9 - - + +
181A TYR* 4.6 3.9 - - + -
190A TRP* 3.9 5.3 - - - -
312A GLU* 3.8 9.1 + - - +
313A PHE* 1.3 69.1 - - - +
315A ARG* 1.3 57.0 + - - +
316A ARG* 3.2 13.3 + - - +
317A ASN* 3.1 30.9 + - - +
318A ASN* 3.1 21.3 + - - -
319A ARG* 2.9 59.6 + - + +
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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