Contacts of the strand formed by residues 376 - 383 (chain A) in PDB entry 2A8L
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 SER 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLY 3.0 21.6 + - - -
52A TYR 3.7 2.9 + - - -
53A HIS* 3.5 27.7 + - - -
372A HIS* 3.6 3.4 - - - -
374A THR* 2.7 22.8 + - - -
375A GLU* 1.3 79.9 - - - +
377A MET* 1.3 63.2 + - - +
393A ILE* 4.2 5.5 - - - +
394A SER 2.9 15.9 - - - -
395A ARG* 3.4 18.2 - - - -
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Residues in contact with MET 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A HIS* 3.8 35.7 - - + +
49A GLY 3.3 13.0 - - - +
50A ALA* 4.1 10.1 - - + -
291A SER* 4.5 2.0 - - - -
342A GLY* 3.7 15.5 - - - -
343A VAL 3.7 36.1 - - - +
344A ILE* 4.4 0.4 - - + -
370A TRP* 4.7 3.6 - - - -
371A SER 4.1 3.8 - - - +
372A HIS* 3.8 24.0 - - + -
376A SER* 1.3 82.3 - - - +
378A CYS* 1.3 65.1 + - - +
379A VAL* 3.7 18.3 + - + +
392A HIS 3.7 0.9 - - - +
393A ILE* 4.6 1.6 - - - -
394A SER* 2.8 33.5 + - - -
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Residues in contact with CYS 378 (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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47A HIS* 3.1 7.3 - - - +
48A ALA* 2.9 34.5 + - + -
49A GLY 3.5 7.6 + - - +
61A TYR* 3.7 21.5 - - + -
62A LYS* 3.6 33.4 - - - -
65A CYS* 3.9 6.7 - - - -
377A MET* 1.3 72.4 - - - +
379A VAL* 1.3 64.4 - - - +
392A HIS 3.6 5.2 - - - -
393A ILE* 3.3 31.8 - - + +
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Residues in contact with VAL 379 (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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45A LEU* 4.3 5.8 - - + -
46A VAL 3.1 12.3 - - - +
47A HIS* 4.1 6.1 - - + +
65A CYS* 4.1 6.2 - - - +
344A ILE* 4.2 4.0 - - + -
370A TRP* 3.9 54.1 - - + +
377A MET* 4.0 21.5 - - + +
378A CYS* 1.3 82.2 - - - +
380A GLY* 1.3 60.9 + - - +
381A TYR* 5.0 2.0 - - + -
391A THR* 3.4 5.4 - - - -
392A HIS* 2.9 49.4 + - + +
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Residues in contact with GLY 380 (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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45A LEU* 3.3 2.8 - - - +
46A VAL* 2.7 42.6 + - - +
65A CYS* 4.1 8.3 - - - -
69A CYS* 3.4 11.1 - - - -
379A VAL* 1.3 76.7 - - - +
381A TYR* 1.3 63.1 + - - +
390A LYS 3.2 11.9 - - - -
391A THR* 4.1 2.2 - - - -
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Residues in contact with TYR 381 (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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43A PHE* 3.7 15.7 - + + -
44A VAL 3.2 13.9 - - - +
45A LEU* 3.8 7.9 - - + -
69A CYS* 3.6 4.6 - - - -
368A PHE* 3.8 26.7 - + - -
370A TRP* 3.7 37.5 - + - -
379A VAL* 5.0 3.6 - - + -
380A GLY* 1.3 80.0 - - - +
382A MET* 1.3 64.2 + - - +
389A ALA* 3.5 0.9 - - - +
390A LYS* 2.8 82.9 + - + +
392A HIS* 5.4 5.4 - - + -
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Residues in contact with MET 382 (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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43A PHE* 3.3 7.9 - - - -
44A VAL* 3.0 33.7 + - + +
69A CYS* 2.8 51.5 - - + +
70A GLN* 3.2 24.0 - - - +
73A ILE* 3.0 26.5 - - + +
381A TYR* 1.3 79.8 - - - +
383A SER* 1.3 72.2 + - - +
387A GLY* 4.3 6.3 - - - -
388A LYS 4.2 20.0 - - - +
389A ALA* 4.0 20.2 - - - -
390A LYS* 6.0 1.6 - - - +
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Residues in contact with SER 383 (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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42A GLY 3.6 6.5 + - - -
43A PHE* 4.0 4.2 - - - -
73A ILE* 4.3 0.4 - - - -
382A MET* 1.3 79.7 - - - +
384A ALA* 1.3 65.8 + - - +
385A GLN* 3.9 12.6 + - - +
386A ASP* 4.1 16.0 + - - +
387A GLY* 2.9 26.7 + - - -
390A LYS* 5.9 2.3 - - - +
413A CYS* 3.2 33.2 - - - -
414A ARG 4.9 3.3 + - - -
415A LEU* 4.9 2.4 - - - +
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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