Contacts of the strand formed by residues 214 - 219 (chain B) in PDB entry 2AX1
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 PRO 214 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B TRP* 3.5 66.7 - - + +
211B LYS* 3.7 15.0 - - + +
212B LYS 3.4 8.7 - - - +
213B ASN* 1.3 88.5 - - - +
215B MET* 1.3 57.7 + - - +
323B ILE* 4.8 0.2 - - + -
324B CYS 3.6 7.2 - - - +
358B TYR* 3.6 20.2 - - - +
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Residues in contact with MET 215 (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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208B TRP* 3.9 4.0 - - - -
214B PRO* 1.3 76.0 - - - +
216B GLY* 1.3 86.0 + - - +
217B PHE* 3.9 9.9 - - + -
308B LEU* 5.4 2.0 - - + -
323B ILE* 3.4 2.8 - - - +
324B CYS* 2.8 52.8 + - - +
326B SER* 4.0 11.2 - - - -
332B ASP* 3.5 36.8 - - + +
335B SER* 4.7 3.1 - - - +
336B LEU* 3.5 28.3 - - + -
356B PRO* 4.1 10.8 - - + -
357B GLU 3.3 9.2 - - - +
358B TYR* 3.5 22.0 - - + +
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Residues in contact with GLY 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B TRP* 3.8 3.9 - - - -
215B MET* 1.3 80.8 - - - +
217B PHE* 1.3 62.3 + - - +
322B VAL 3.0 12.1 - - - -
323B ILE* 4.2 1.1 - - - -
357B GLU* 2.8 38.2 + - - +
363B ILE* 3.8 21.1 - - - -
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Residues in contact with PHE 217 (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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215B MET* 3.9 10.5 - - + -
216B GLY* 1.3 78.4 - - - +
218B SER* 1.3 72.5 + - - +
219B TYR* 4.3 6.2 + - + -
308B LEU* 4.1 18.2 - - + -
321B VAL* 3.4 5.4 - - - +
322B VAL* 2.9 67.5 + - + +
324B CYS* 5.2 0.7 - - - -
336B LEU* 3.8 29.8 - - + -
339B PHE* 3.8 37.5 - + - -
354B PRO* 3.9 11.7 - - + -
355B GLN 3.5 24.0 - - - +
356B PRO* 4.5 0.4 - - + -
357B GLU* 5.3 0.2 - - - -
363B ILE* 4.3 6.2 - - - +
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Residues in contact with SER 218 (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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217B PHE* 1.3 78.2 - - - +
219B TYR* 1.3 60.4 + - - +
220B ASP* 4.1 1.8 + - - +
319B ASP* 6.5 0.2 - - - -
320B LEU 3.1 12.3 - - - -
321B VAL* 4.2 1.1 - - - +
354B PRO* 3.6 21.8 - - - +
355B GLN 4.8 1.9 + - - +
363B ILE* 4.8 5.8 - - - +
364B THR* 3.3 29.6 + - - -
365B SER* 4.6 6.5 - - - -
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Residues in contact with TYR 219 (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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217B PHE* 4.3 4.0 + - + -
218B SER* 1.3 74.3 - - - +
220B ASP* 1.3 60.3 + - - +
221B THR* 3.4 30.6 + - - -
295B CYS* 6.2 0.4 - - - -
318B ASP 4.1 13.0 - - - +
320B LEU* 3.0 38.7 + - + +
339B PHE* 3.6 24.5 - + + -
340B THR* 3.8 23.4 + - - +
343B MET* 3.4 30.5 - - + +
348B ALA 2.8 24.1 + - - -
349B PRO* 3.8 0.2 - - - +
350B PRO* 3.1 32.9 - - + +
352B ASP 5.6 0.4 - - - -
354B PRO* 4.0 17.7 - - + -
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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