Contacts of the strand formed by residues 309 - 314 (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 PHE 309 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B TYR* 3.7 46.2 - + + -
268B THR 4.0 12.3 - - - -
269B LEU* 4.1 11.2 - - + -
305B PHE* 3.0 44.4 + + + +
306B ILE* 3.1 17.9 + - - +
308B LYS* 1.4 98.7 - - + +
310B TYR* 1.3 54.9 + - - +
311B THR* 2.8 25.8 + - - -
322B PHE* 4.1 11.4 - - + -
323B ALA 3.3 17.9 - - - +
324B LEU* 3.9 19.7 - - + -
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Residues in contact with TYR 310 (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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152B SER* 3.2 33.9 - - - -
153B PHE 3.7 13.2 - - - -
154B TYR* 3.6 28.9 - + + +
164B GLN* 4.5 0.7 + - - -
166B VAL* 4.0 6.4 - - - +
170B SER* 3.5 13.2 - - - -
171B ASP* 2.8 33.4 + - + +
174B HIS* 3.6 31.2 - - + +
175B TYR* 3.7 19.5 - + + -
179B PHE* 3.6 20.4 - + - -
306B ILE 4.5 1.6 - - - -
309B PHE* 1.3 69.0 - - - +
311B THR* 1.3 59.7 + - - +
321B GLY 3.7 0.7 - - - +
322B PHE* 3.5 5.2 - - - -
323B ALA 2.7 36.7 + - - +
325B ALA* 3.7 10.0 - - + +
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Residues in contact with THR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B PHE 4.2 0.3 - - - +
152B SER* 3.2 3.8 - - - -
153B PHE* 2.8 41.8 + - - +
214B VAL* 4.1 3.8 - - + -
306B ILE* 3.8 16.3 - - - +
309B PHE 2.8 16.2 + - - -
310B TYR* 1.3 73.3 - - - +
312B GLU* 1.3 60.9 + - - +
313B PHE* 3.6 33.5 - - + -
320B ILE* 3.7 12.6 - - + -
321B GLY 3.4 2.5 - - - -
322B PHE* 3.4 29.6 - - + -
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Residues in contact with GLU 312 (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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148B GLU* 5.2 4.1 - - - +
150B VAL* 4.2 32.4 - - + +
151B PHE 3.6 4.7 - - - +
152B SER* 3.5 15.0 - - - +
169B GLY* 5.2 0.2 - - - -
170B SER* 2.8 20.6 + - - -
179B PHE* 4.0 20.5 - - + -
181B TYR* 2.9 34.0 + - - -
310B TYR 4.2 0.4 + - - -
311B THR* 1.3 73.6 - - - +
313B PHE* 1.3 63.5 + - - +
314B ASP* 3.8 4.5 + - - +
320B ILE* 3.4 7.3 - - - +
321B GLY* 2.8 42.3 + - - +
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Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 3.7 19.7 - - + -
150B VAL* 3.2 7.6 - - - -
151B PHE* 2.7 70.6 + + + +
153B PHE* 3.6 23.3 - + - -
190B TRP* 3.6 34.5 - + + -
214B VAL* 3.7 29.2 - - + -
216B THR* 3.8 10.5 - - + -
311B THR* 3.6 27.6 - - + -
312B GLU* 1.3 73.8 - - - +
314B ASP* 1.3 58.6 + - - +
315B ARG 3.7 1.3 + - - -
319B ARG 4.2 1.3 - - - -
320B ILE* 4.0 12.3 - - + -
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Residues in contact with ASP 314 (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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150B VAL* 3.6 19.8 - - + +
181B TYR* 4.5 2.8 - - + -
190B TRP* 3.9 5.6 - - - -
312B GLU* 3.8 9.3 + - - +
313B PHE* 1.3 69.5 - - - +
315B ARG* 1.3 57.6 + - - +
316B ARG* 3.2 13.9 + - - +
317B ASN* 3.2 25.0 + - - +
318B ASN* 3.1 21.1 + - - -
319B ARG* 3.0 67.2 + - - +
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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
------------------------------------------------------------
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