Contacts of the strand formed by residues 309 - 316 (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 GLN 309 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307B LYS 4.3 7.2 - - - +
308B LEU* 1.3 73.6 - - - +
310B ASP* 1.3 70.2 + - + +
324B CYS* 3.1 5.9 - - - +
325B GLU* 3.0 51.1 + - + +
326B SER 3.7 4.0 + - - +
327B ALA* 3.4 33.1 - - + +
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Residues in contact with ASP 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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210B SER* 5.0 3.6 + - - +
211B LYS* 2.8 48.2 + - - +
308B LEU 3.9 1.6 + - - -
309B GLN* 1.3 74.2 - - + +
311B CYS* 1.3 62.4 + - - +
312B THR* 4.8 0.9 + - - -
324B CYS* 3.5 2.4 - - - -
325B GLU* 3.8 19.7 - - + +
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Residues in contact with CYS 311 (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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303B CYS* 3.7 30.7 - - + -
308B LEU* 3.2 45.9 + - - +
309B GLN 3.2 1.4 + - - -
310B ASP* 1.3 78.7 - - - +
312B THR* 1.3 63.0 + - - +
313B MET* 4.2 3.6 - - + -
322B VAL* 4.0 10.1 - - + -
323B ILE 3.8 4.0 - - - -
324B CYS* 4.1 4.5 - - - -
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Residues in contact with THR 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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189B SER* 5.5 1.8 - - - +
190B SER* 5.7 0.7 - - - +
203B PHE* 3.8 28.7 - - + -
207B THR* 3.5 29.4 - - + +
211B LYS* 2.7 26.0 + - - -
310B ASP* 4.8 0.9 + - - -
311B CYS* 1.3 76.2 + - - +
313B MET* 1.3 63.6 + - - +
321B VAL 4.0 0.2 - - - +
322B VAL* 3.5 2.1 - - - -
323B ILE* 2.9 35.5 + - - +
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Residues in contact with MET 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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190B SER* 3.0 31.9 + - - +
203B PHE* 4.2 8.2 - - - -
296B TYR* 3.5 41.1 - - + +
299B ALA* 3.9 12.3 - - + -
300B SER* 3.7 28.9 - - - +
303B CYS* 4.0 15.9 - - - -
311B CYS* 5.1 2.7 - - + -
312B THR* 1.3 81.6 - - - +
314B LEU* 1.3 62.7 + - - +
315B VAL* 3.7 14.4 - - + -
320B LEU* 4.0 7.0 - - + -
321B VAL 3.4 7.6 - - - +
322B VAL* 3.8 16.8 - - + -
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Residues in contact with LEU 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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189B SER 4.0 5.4 - - - +
190B SER 3.4 13.0 - - - +
192B GLY* 3.7 9.9 - - - -
195B TYR* 3.7 29.8 - - + -
200B ARG* 3.4 43.4 + - + +
203B PHE* 4.0 15.5 - - + -
204B LEU* 3.7 27.8 - - + -
313B MET* 1.3 73.0 - - - +
315B VAL* 1.3 63.0 + - - +
316B ASN* 4.3 1.5 - - - +
319B ASP 3.9 0.9 - - - +
320B LEU* 3.7 1.4 - - - -
321B VAL* 3.0 40.8 + - + +
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Residues in contact with VAL 315 (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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187B MET* 5.3 0.9 - - - -
190B SER 2.7 15.8 + - - +
191B TYR* 4.5 0.3 - - - -
192B GLY 2.9 25.8 + - - -
193B PHE 4.6 0.2 + - - -
292B THR* 3.9 25.2 - - + +
295B CYS* 3.9 20.2 - - + -
296B TYR* 4.2 13.9 - - + -
313B MET* 3.7 31.4 - - + -
314B LEU* 1.3 80.5 - - - +
316B ASN* 1.3 67.2 + - - +
317B GLY 3.3 20.4 - - - +
319B ASP 3.4 7.2 - - - +
320B LEU* 3.9 7.0 - - + -
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Residues in contact with ASN 316 (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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192B GLY* 3.5 26.7 + - - -
193B PHE* 3.6 34.5 - - + -
200B ARG* 2.9 32.1 + - - +
314B LEU* 4.3 2.9 - - - +
315B VAL* 1.3 81.2 - - - +
317B GLY* 1.3 59.5 + - - +
318B ASP* 3.2 1.0 + - - +
319B ASP* 2.9 35.0 + - - +
366B CYS* 4.0 19.2 - - - -
448B TYR* 4.8 0.2 + - - -
1002B 5EE 3.8 13.3 - - - -
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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