Contacts of the helix formed by residues 302 - 308 (chain B) 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 GLY 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ASP 3.3 9.9 - - - -
218B ALA* 3.3 12.6 - - - -
220B TYR 3.2 24.9 + - - -
221B ILE* 4.4 1.0 - - - +
300B ALA 3.5 0.8 + - - -
301B LEU* 1.3 76.4 - - - +
303B ALA* 1.3 65.0 - - - -
304B THR 3.2 3.1 - - - -
305B PHE* 2.9 13.2 + - - +
306B ILE* 3.1 16.0 + - - +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASP 4.1 1.8 - - - +
12B THR 5.3 1.1 - - - +
14B TYR* 3.8 20.4 - - + -
155B TYR* 3.8 19.3 - - + -
215B ASP 4.4 0.6 + - - -
216B THR 5.3 0.2 - - - +
218B ALA 2.9 13.3 + - - +
219B SER* 3.3 19.4 + - - +
302B GLY* 1.3 69.6 - - - -
304B THR* 1.3 57.4 + - - +
306B ILE* 3.2 1.2 + - - +
307B ARG* 2.9 52.9 + - - +
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Residues in contact with THR 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B SER 3.5 3.7 + - - -
220B TYR* 3.4 10.0 - - - -
221B ILE* 3.9 23.1 - - + -
269B LEU* 4.2 13.5 - - + +
273B ASP* 3.7 24.4 - - - +
274B TYR* 4.3 6.5 - - + -
285B ALA* 2.9 44.2 + - + +
286B ILE* 5.2 0.2 - - + -
302B GLY 3.1 0.6 + - - -
303B ALA* 1.3 76.5 - - - +
305B PHE* 1.3 60.5 + - - +
307B ARG* 3.6 22.0 + - - +
308B LYS* 4.1 3.5 + - - +
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Residues in contact with PHE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B VAL* 5.9 0.2 - - + -
221B ILE* 4.0 15.0 - - + +
260B PHE* 4.1 21.5 - + - -
262B LEU* 3.9 14.4 - - + -
267B TYR* 3.8 29.2 - + + -
269B LEU* 4.7 7.2 - - + -
301B LEU* 3.8 38.1 - - + -
302B GLY 2.9 9.8 + - - +
304B THR* 1.3 79.0 - - - +
306B ILE* 1.4 65.0 + - + +
307B ARG 3.3 0.2 - - - -
308B LYS* 3.2 5.0 + - - +
309B PHE* 3.0 51.7 + + + -
322B PHE* 3.6 35.0 - + - -
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B PHE* 4.1 25.8 - - + +
154B TYR* 5.5 0.3 - - - -
155B TYR* 3.7 34.8 + - + +
214B VAL* 4.5 9.4 - - + -
215B ASP 4.4 0.4 - - - -
216B THR* 3.8 39.7 - - + +
301B LEU 4.0 12.3 - - - +
302B GLY 3.1 17.2 + - - +
305B PHE* 1.4 76.6 - - + +
307B ARG* 1.3 64.4 + - - +
309B PHE 3.1 28.2 + - - +
310B TYR* 4.0 2.3 + - - -
311B THR* 3.8 15.5 - - - +
325B ALA* 4.7 1.4 - - - +
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ASP* 2.8 44.7 + - - +
14B TYR* 2.8 37.0 + - - +
154B TYR* 5.4 0.5 - - - -
155B TYR* 3.5 26.5 - - + +
156B ASN 3.5 9.4 - - - -
157B ARG* 3.5 44.4 + - + +
219B SER 4.8 0.6 + - - -
273B ASP 4.9 7.1 + - - -
276B PHE* 4.2 14.6 - - - -
285B ALA* 4.4 3.0 - - - +
303B ALA* 2.9 20.7 + - - +
304B THR* 3.6 36.8 + - - +
305B PHE 3.3 0.2 - - - -
306B ILE* 1.3 77.2 - - - +
308B LYS* 1.4 58.6 + - - +
325B ALA* 3.6 10.4 - - - +
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Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ARG* 4.1 14.1 + - - +
268B THR* 3.0 26.3 + - - +
269B LEU* 3.8 14.6 - - + -
270B THR* 4.2 12.7 - - - +
273B ASP* 3.0 36.9 + - + +
304B THR 4.1 2.8 + - - +
305B PHE 3.2 8.4 + - - +
307B ARG* 1.4 79.8 - - - +
309B PHE* 1.4 75.6 + - + +
324B LEU* 3.7 24.1 - - + +
325B ALA* 2.9 25.0 + - - +
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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