Contacts of the strand formed by residues 309 - 316 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A LYS 4.2 7.7 + - - +
308A LEU* 1.3 73.0 - - - +
310A ASP* 1.3 69.3 + - + +
324A CYS* 3.2 5.1 - - - +
325A GLU* 3.0 52.5 + - + +
326A SER 4.6 2.4 + - - +
327A ALA* 3.7 29.7 - - - +
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Residues in contact with ASP 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A SER* 5.0 4.9 + - - +
211A LYS* 2.8 44.5 + - - +
308A LEU 3.8 1.8 + - - -
309A GLN* 1.3 75.6 - - + +
311A CYS* 1.3 59.3 + - - +
312A THR* 4.8 0.5 + - - -
324A CYS* 3.5 3.6 - - - -
325A GLU* 4.0 17.6 - - + +
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Residues in contact with CYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A CYS* 3.8 23.3 - - + -
308A LEU* 3.1 52.7 + - - +
309A GLN 3.3 1.2 + - - -
310A ASP* 1.3 79.0 - - - +
312A THR* 1.3 64.2 + - - +
313A MET* 5.2 3.1 - - + -
322A VAL* 4.0 9.9 - - + -
323A ILE 3.6 3.6 - - - -
324A CYS* 4.0 5.4 - - - -
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Residues in contact with THR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A SER* 5.7 0.9 - - - +
190A SER* 5.5 0.9 - - - +
203A PHE* 3.7 29.4 - - + -
207A THR* 3.4 28.9 - - + +
211A LYS* 2.8 26.7 + - - -
310A ASP* 4.8 0.9 + - - -
311A CYS* 1.3 74.9 + - - +
313A MET* 1.3 64.1 + - - +
321A VAL 3.8 0.7 - - - +
322A VAL* 3.4 2.5 - - - +
323A ILE* 2.9 34.5 + - - +
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Residues in contact with MET 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A SER* 2.9 30.8 + - - +
203A PHE* 4.2 6.9 - - - -
296A TYR* 3.4 35.2 - - + +
299A ALA* 3.8 14.1 - - + -
300A SER* 3.3 43.3 - - - +
303A CYS* 4.0 13.9 - - - -
311A CYS* 5.2 2.5 - - + -
312A THR* 1.3 81.9 - - - +
314A LEU* 1.3 60.9 + - - +
315A VAL* 3.9 12.1 - - + -
320A LEU* 4.3 7.0 - - + -
321A VAL 3.4 7.0 - - - +
322A VAL* 4.1 12.3 - - + -
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A SER 4.0 1.1 - - - +
190A SER 3.6 12.8 - - - +
192A GLY* 3.8 18.8 - - - -
195A TYR* 3.8 19.7 - - + -
200A ARG* 3.5 43.3 + - + +
203A PHE* 4.0 19.7 - - + -
204A LEU* 3.8 28.7 - - + -
313A MET* 1.3 74.4 - - - +
315A VAL* 1.3 61.2 + - - +
316A ASN* 4.2 1.1 - - - +
319A ASP* 3.9 1.2 - - - +
320A LEU* 3.7 3.3 - - - -
321A VAL* 3.0 41.9 + - + +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A MET* 5.3 0.2 - - - -
190A SER 2.8 14.4 + - - +
191A TYR* 4.5 0.5 - - - -
192A GLY 2.9 26.0 + - - -
292A THR* 3.7 32.4 - - + +
295A CYS* 3.9 11.7 - - + -
296A TYR* 4.2 13.2 - - + -
313A MET* 3.9 20.9 - - + -
314A LEU* 1.3 78.7 - - - +
316A ASN* 1.3 65.2 + - - +
317A GLY 3.4 20.6 - - - +
319A ASP 3.4 6.7 - - - +
320A LEU* 3.7 19.1 - - + -
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Residues in contact with ASN 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLY* 3.4 29.4 + - - -
193A PHE* 3.7 32.8 - - + -
200A ARG* 2.8 32.7 + - - +
314A LEU* 4.2 2.6 - - - +
315A VAL* 1.3 80.2 - - - +
317A GLY* 1.3 64.9 + - - +
318A ASP* 3.1 1.4 + - - +
319A ASP* 2.9 28.7 + - + +
366A CYS* 4.0 17.1 - - - -
1001A 5EE 3.9 15.6 - - - -
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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