Contacts of the strand formed by residues 369 - 378 (chain A) in PDB entry 1ADI
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 GLU 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A TYR* 3.3 2.5 - - - -
348A ARG* 2.5 69.9 + - + +
367A GLY 3.4 4.9 + - - +
368A VAL* 1.3 72.9 - - - +
370A PRO* 1.4 74.5 - - + +
371A ILE* 4.5 0.5 - - - +
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Residues in contact with PRO 370 (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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279A PRO* 3.4 23.6 - - + +
280A THR* 4.6 0.2 - - - +
344A CYS* 3.8 15.0 - - - -
346A ALA 3.8 5.8 - - - +
347A TYR* 4.2 6.3 - - + -
348A ARG* 6.2 0.7 - - - -
368A VAL 4.0 4.5 - - - +
369A GLU* 1.4 95.6 - - + +
371A ILE* 1.3 62.2 + - - +
372A TYR* 3.3 46.3 + - + +
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Residues in contact with ILE 371 (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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344A CYS* 3.7 1.3 - - - -
345A VAL* 3.1 32.9 + - + +
346A ALA* 2.9 38.4 + - + +
347A TYR 4.4 6.5 - - - +
348A ARG* 4.0 16.4 - - - +
354A GLU* 3.3 42.8 - - + +
369A GLU 4.5 2.2 - - - +
370A PRO* 1.3 71.3 - - - +
372A TYR* 1.3 66.7 + - - +
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Residues in contact with TYR 372 (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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279A PRO 3.9 0.2 + - - -
280A THR* 3.3 48.0 + - - -
281A GLU 4.5 2.9 + - - -
282A LEU* 5.1 2.3 - - + +
309A TRP* 3.7 31.0 - + + -
342A LYS* 3.9 31.4 - - + -
343A LEU 3.8 1.6 - - - -
344A CYS* 3.9 19.3 - - + -
345A VAL* 4.8 1.8 - - - -
370A PRO* 3.3 34.5 - - + +
371A ILE* 1.3 80.2 - - - +
373A GLU* 1.3 61.3 + - - +
374A THR* 4.1 5.1 + - - +
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Residues in contact with GLU 373 (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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342A LYS* 3.1 7.3 - - - +
343A LEU* 3.0 45.6 + - + +
345A VAL* 3.7 27.5 - - + +
371A ILE 4.1 0.4 + - - -
372A TYR* 1.3 73.0 - - - +
374A THR* 1.3 66.5 + - - +
375A MET* 5.5 3.4 - - + -
401A ARG* 2.6 42.1 + - - -
405A LEU* 4.9 1.2 - - - +
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Residues in contact with THR 374 (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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340A GLU* 3.1 38.1 - - + +
341A VAL 3.7 7.2 - - - +
342A LYS* 4.5 12.7 - - + +
372A TYR* 4.2 4.9 + - - +
373A GLU* 1.3 77.7 - - - +
375A MET* 1.3 71.9 + - - +
376A PRO* 4.7 1.3 - - - +
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Residues in contact with MET 375 (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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340A GLU* 3.6 2.6 - - - -
341A VAL* 2.7 58.9 + - + +
343A LEU* 3.7 23.3 - - + -
373A GLU* 5.5 4.3 - - + -
374A THR* 1.3 84.0 - - - +
376A PRO* 1.3 69.2 - - + +
394A ALA 5.0 2.2 - - - +
397A ASN* 3.0 39.9 - - + +
398A TYR* 3.2 24.2 - - + +
401A ARG* 3.6 25.4 - - + -
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Residues in contact with PRO 376 (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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339A LYS 3.5 8.7 - - - +
340A GLU* 4.6 3.8 - - + -
341A VAL* 4.1 4.3 - - - +
374A THR 4.7 1.6 - - - +
375A MET* 1.3 91.2 - - + +
377A GLY* 1.3 65.7 + - - +
378A TRP* 4.5 2.6 - - - -
394A ALA* 4.2 12.7 - - + +
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Residues in contact with GLY 377 (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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335A LEU 5.5 0.4 - - - -
338A LEU* 4.3 7.2 - - - -
339A LYS* 2.7 25.1 + - - +
341A VAL* 4.3 11.4 - - - -
375A MET 3.5 1.6 + - - -
376A PRO* 1.3 78.8 - - - +
378A TRP* 1.3 73.4 + - - -
379A SER* 4.4 0.5 + - - -
394A ALA* 3.6 8.5 - - - +
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Residues in contact with TRP 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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332A LEU* 3.8 29.1 - - + +
335A LEU* 3.7 32.5 + - + -
336A ASP* 2.3 42.0 + - - +
337A GLY 3.4 16.8 + - - -
338A LEU 3.8 7.8 + - - +
341A VAL* 4.2 21.3 - - + -
376A PRO 4.7 0.7 - - - -
377A GLY* 1.3 80.8 - - - -
379A SER* 1.3 60.5 + - - +
380A GLU* 3.8 13.0 - - - +
382A THR* 4.6 3.1 + - - -
392A PRO* 3.9 35.4 - - + -
394A ALA* 3.8 14.4 - - + -
395A ALA* 3.4 31.3 - - + +
398A TYR* 4.0 18.8 - + + -
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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