Contacts of the strand formed by residues 360 - 368 (chain A) in PDB entry 2ADU
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 VAL 360 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A TRP* 4.6 5.8 - - + -
169A PHE* 3.6 25.8 - - + -
332A SER* 3.3 6.4 - - - -
333A ILE* 2.8 53.8 + - + +
358A GLY 4.6 6.1 - - - +
359A GLU* 1.3 78.4 - - - +
361A TYR* 1.3 64.9 + - - +
461A THR* 3.7 22.0 - - + -
462A ILE 3.5 10.5 - - - +
463A LEU* 3.5 23.1 - - + -
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Residues in contact with TYR 361 (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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297A LEU* 4.1 7.1 - - + +
331A HIS 3.5 1.6 - - - -
332A SER* 3.9 23.3 - - - -
333A ILE* 4.6 4.3 - - - -
342A LYS* 2.9 28.7 - - + +
344A VAL* 3.5 27.6 - - + -
355A MET* 3.6 29.9 - - + +
359A GLU* 2.7 40.8 + - + -
360A VAL* 1.3 80.0 - - - +
362A ALA* 1.3 59.2 + - - +
363A ILE* 3.6 10.0 + - + -
461A THR* 3.3 3.6 - - - +
462A ILE* 2.8 52.9 + - + +
464A LEU* 3.9 24.0 - - + -
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Residues in contact with ALA 362 (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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262A ASP* 3.9 6.1 - - + +
330A GLY* 3.2 7.1 - - - -
331A HIS* 2.6 68.9 + - + +
333A ILE* 4.0 10.9 - - + +
344A VAL* 4.6 0.3 - - - +
361A TYR* 1.3 71.8 - - - +
363A ILE* 1.3 63.8 + - - +
364A GLU* 3.7 0.6 - - - +
459A GLU* 3.6 10.5 - - - +
460A HIS 3.5 7.0 - - - +
461A THR* 4.4 2.0 - - - +
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Residues in contact with ILE 363 (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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284A THR* 3.8 13.9 - - + +
287A GLY* 3.9 9.0 - - - +
288A ILE* 3.8 36.8 - - + +
291A ALA* 4.5 4.9 - - + -
300A VAL* 5.5 0.4 - - + -
304A ILE* 5.0 8.5 - - + -
330A GLY* 4.8 1.1 - - - -
344A VAL* 4.4 14.6 - - + -
355A MET* 4.2 14.4 - - + -
361A TYR* 4.0 10.5 - - + -
362A ALA* 1.3 75.3 - - - +
364A GLU* 1.3 60.2 + - - +
365A THR* 5.2 0.9 - - + -
459A GLU* 3.2 2.6 - - - -
460A HIS 2.8 32.7 + - - +
462A ILE* 3.7 41.7 - - + -
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Residues in contact with GLU 364 (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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251A ASP* 4.2 0.3 - - - +
304A ILE* 5.6 0.2 - - - +
329A ASN* 3.5 20.4 - - - +
330A GLY* 3.8 11.5 + - - -
331A HIS* 2.8 12.5 + - - -
346A ILE* 3.4 15.8 - - - +
362A ALA 3.5 1.8 + - - +
363A ILE* 1.3 75.7 - - - +
365A THR* 1.3 65.1 + - - +
366A PHE* 3.2 16.2 - - + -
457A GLN* 2.8 30.9 + - + +
458A PHE 3.3 4.9 - - - +
459A GLU* 2.4 29.2 - - + +
502A CO 1.9 27.7 + - - -
906A R20 3.2 6.2 + - - -
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Residues in contact with THR 365 (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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280A VAL* 3.4 17.9 + - - +
284A THR* 2.7 34.9 + - + +
304A ILE* 3.4 42.0 - - + -
308A MET* 3.9 8.3 - - - +
346A ILE* 3.8 10.5 - - + -
363A ILE* 5.2 1.6 - - + -
364A GLU* 1.3 80.2 - - - +
366A PHE* 1.3 65.7 + - - +
457A GLN* 3.4 21.8 - - - +
458A PHE 3.3 8.4 + - - -
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Residues in contact with PHE 366 (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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229A ALA* 3.5 28.0 - - + -
230A ALA* 4.2 9.9 - - + -
249A LYS* 5.5 0.2 - - + -
308A MET* 3.4 5.9 - - - +
324A PRO* 3.3 7.8 - - - +
325A ILE* 3.1 44.6 + - + -
328A LEU* 3.6 39.9 - - + -
329A ASN 4.8 3.1 - - - -
346A ILE* 3.7 7.2 - - + +
364A GLU* 3.2 28.3 - - + -
365A THR* 1.3 80.8 - - - +
367A GLY* 1.3 59.4 + - - +
456A ALA 3.2 7.6 - - - +
457A GLN* 3.1 50.9 - - + -
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Residues in contact with GLY 367 (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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276A LEU* 4.3 7.4 - - - +
280A VAL* 3.7 20.4 - - - +
308A MET* 3.9 9.4 - - - -
322A VAL* 4.0 2.7 - - - -
323A LYS 3.5 5.8 - - - -
325A ILE* 4.6 0.4 - - - -
366A PHE* 1.3 73.9 - - - +
368A SER* 1.3 61.1 + - - -
455A THR* 3.0 6.6 - - - -
456A ALA 2.8 33.0 + - - -
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Residues in contact with SER 368 (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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276A LEU* 5.0 1.8 - - - -
321A GLN 4.6 0.5 - - - +
322A VAL* 4.2 5.4 - - - +
323A LYS* 2.9 40.7 + - - +
325A ILE* 4.0 12.1 - - - -
367A GLY* 1.3 76.4 - - - -
369A THR* 1.3 60.4 + - - +
370A GLY* 2.8 17.5 + - - -
372A GLY* 4.7 4.0 - - - -
449A ASP* 2.9 23.2 + - - +
453A SER* 4.3 0.7 + - - -
454A TYR 3.1 8.3 + - - -
455A THR* 3.6 16.4 - - - +
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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