Contacts of the strand formed by residues 309 - 314 (chain B) in PDB entry 2ANL
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 309 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B THR 4.8 1.0 + - - -
266B TYR* 3.7 18.7 - + + -
267B THR* 2.8 42.4 + - - -
305B PHE* 2.9 61.9 + + + +
306B MET* 3.3 17.9 - - - +
308B LYS* 1.3 94.3 + - + +
310B PHE* 1.3 66.8 + - - +
311B THR* 3.1 15.8 + - + +
322B PHE* 5.2 1.8 - - + -
323B ALA* 3.2 29.6 - - - +
324B VAL* 3.7 22.7 - - + -
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Residues in contact with PHE 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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155B THR* 3.2 43.3 - - + -
156B PHE 3.5 17.3 - - - -
157B TYR* 3.8 15.7 - - + +
173B ILE* 4.4 4.5 - - + -
174B GLU 4.7 6.1 - - - -
177B PHE* 3.8 24.5 - + + +
178B TYR* 3.7 42.4 - + + -
182B LEU* 5.0 1.1 - - + -
306B MET 4.8 1.3 - - - -
309B TYR* 1.3 67.8 - - - +
311B THR* 1.3 59.3 + - - +
312B VAL* 3.5 20.2 - - + -
321B GLY 4.8 0.2 - - - -
322B PHE* 3.8 1.2 - - - -
323B ALA* 2.6 42.5 + - + +
325B ALA* 3.6 24.2 - - + +
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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
----------------------------------------------------------
155B THR* 3.5 5.4 - - - -
156B PHE* 3.0 47.6 + - - +
213B VAL* 4.9 2.0 - - + -
305B PHE* 4.5 14.6 - - + -
306B MET* 3.8 16.6 - - + +
309B TYR* 3.1 23.5 + - + +
310B PHE* 1.3 75.9 - - - +
312B VAL* 1.3 64.3 + - - +
313B PHE* 3.4 17.2 - - + -
320B ILE* 4.5 5.8 - - + -
321B GLY 3.4 7.6 - - - +
322B PHE* 4.6 6.3 - - + -
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 4.6 7.2 - - + -
154B PHE 4.0 2.2 - - - -
155B THR* 3.9 13.9 - - + -
173B ILE* 4.1 20.0 - - + -
182B LEU* 3.8 22.2 - - + -
184B TYR* 5.3 6.3 - - + -
310B PHE* 3.5 29.2 - - + +
311B THR* 1.3 76.4 - - - +
313B PHE* 1.3 71.5 + - - +
314B ASP* 4.1 3.8 + - + +
320B ILE* 2.9 6.6 - - - +
321B GLY* 2.5 49.4 + - - +
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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
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35B THR* 4.5 10.8 - - + -
153B LEU* 2.7 35.7 - - - +
154B PHE* 3.0 54.5 + + + +
156B PHE* 4.1 10.8 - + - -
193B TRP* 3.5 42.5 - + + -
213B VAL* 3.8 30.3 - - + -
306B MET* 5.0 3.8 - - + -
311B THR* 3.4 28.3 - - - -
312B VAL* 1.3 75.3 - - - +
314B ASP* 1.3 53.1 + - - +
319B SER 4.0 0.9 - - - -
320B ILE* 3.4 22.2 - - + +
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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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151B GLN* 5.2 3.5 - - - +
152B ALA 3.4 8.5 - - - +
153B LEU* 3.2 27.5 - - + +
184B TYR* 5.7 2.7 - - + -
193B TRP* 3.6 4.4 - - - -
312B VAL* 4.1 5.0 + - + +
313B PHE* 1.3 73.2 - - - +
315B TYR* 1.3 69.2 + - - +
316B ASP* 3.6 6.8 + - - +
317B LYS* 2.9 60.7 + - + +
318B GLU* 2.9 12.1 + - - -
319B SER 2.7 22.9 + - - +
320B ILE* 5.6 0.2 - - - -
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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
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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