Contacts of the strand formed by residues 369 - 378 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347B TYR* 3.5 1.2 - - - -
348B ARG* 3.0 62.9 + - + +
367B GLY 3.9 7.6 - - - +
368B VAL* 1.3 83.1 - - - +
370B PRO* 1.3 73.5 - - + +
371B ILE 3.4 1.0 + - - -
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Residues in contact with PRO 370 (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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279B PRO* 3.9 25.8 - - + +
280B THR* 4.4 4.3 - - + -
344B CYS* 3.6 17.9 - - - -
346B ALA 3.5 7.2 - - - +
347B TYR* 4.8 2.5 - - + -
348B ARG* 4.7 1.2 + - - -
368B VAL* 4.5 1.7 - - - +
369B GLU* 1.3 87.9 - - + +
371B ILE* 1.3 64.4 + - - +
372B TYR* 3.0 53.6 + - + +
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Residues in contact with ILE 371 (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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345B VAL* 3.0 40.6 + - + +
346B ALA* 2.9 25.2 + - + +
348B ARG* 3.1 65.1 - - + +
354B GLU* 3.9 26.2 - - + +
369B GLU 4.1 1.3 - - - +
370B PRO* 1.3 71.8 - - - +
372B TYR* 1.3 63.0 + - - +
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Residues in contact with TYR 372 (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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279B PRO 3.9 0.7 + - - -
280B THR* 3.3 49.2 + - + +
281B GLU 5.2 0.2 + - - -
282B LEU* 4.9 3.1 - - + +
309B TRP* 3.8 22.5 - + + -
342B LYS* 4.1 31.6 - - + -
343B LEU 3.7 4.3 - - - -
344B CYS* 3.7 20.0 - - + -
345B VAL* 4.5 1.5 - - - +
370B PRO* 3.0 36.1 + - + +
371B ILE* 1.3 79.6 - - - +
373B GLU* 1.3 61.0 + - - +
374B THR* 4.1 5.5 + - + +
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Residues in contact with GLU 373 (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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342B LYS* 3.3 3.1 - - - -
343B LEU* 3.1 36.5 + - + +
345B VAL* 3.7 18.4 - - + +
371B ILE 4.0 0.2 + - - -
372B TYR* 1.3 72.7 - - - +
374B THR* 1.3 67.7 + - - +
375B MET* 4.1 14.5 + - + +
401B ARG* 2.8 54.0 + - - +
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Residues in contact with THR 374 (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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340B GLU* 4.6 19.4 + - + +
341B VAL 3.6 3.1 - - - -
342B LYS* 3.3 38.6 - - + -
372B TYR* 4.1 6.7 + - + -
373B GLU* 1.3 77.9 - - - +
375B MET* 1.3 63.6 + - - +
376B PRO* 4.8 0.2 - - - +
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Residues in contact with MET 375 (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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340B GLU* 3.4 8.0 - - - +
341B VAL* 2.7 50.2 + - + +
342B LYS* 5.3 0.4 - - - -
343B LEU* 4.0 24.0 - - - -
373B GLU* 4.3 20.4 - - + +
374B THR* 1.3 75.9 - - - +
376B PRO* 1.4 74.8 - - + +
394B ALA 5.1 1.3 - - - +
397B ASN* 3.6 16.2 - - + +
398B TYR* 3.3 50.5 - - + +
401B ARG* 4.1 6.5 - - + -
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Residues in contact with PRO 376 (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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339B LYS 3.9 5.2 - - - +
340B GLU* 4.6 3.1 - - + -
341B VAL* 4.6 3.8 - - - +
374B THR 4.8 0.2 - - - +
375B MET* 1.4 98.2 - - + +
377B GLY* 1.3 67.6 + - - +
378B TRP* 4.4 4.9 - - - -
394B ALA* 4.4 13.7 - - + +
397B ASN* 6.4 0.2 - - - +
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Residues in contact with GLY 377 (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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338B LEU 3.1 20.2 - - - -
339B LYS 2.7 17.1 + - - -
340B GLU* 4.4 2.7 - - - -
341B VAL* 4.6 7.2 - - - -
375B MET 3.8 0.2 + - - -
376B PRO* 1.3 80.5 - - - +
378B TRP* 1.3 70.3 + - - +
394B ALA* 3.8 8.3 - - - +
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Residues in contact with TRP 378 (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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332B LEU* 3.8 37.0 - - + -
335B LEU* 3.7 35.2 + - + -
336B ASP* 2.5 31.8 + - - +
337B GLY* 2.9 24.1 + - - -
338B LEU 3.4 7.0 + - - +
341B VAL* 4.3 17.7 - - + -
376B PRO 4.4 2.5 - - - -
377B GLY* 1.3 82.2 - - - +
379B SER* 1.3 59.8 + - - +
380B GLU* 3.5 24.2 - - - +
382B THR* 3.9 6.0 - - + +
392B PRO* 4.1 17.3 - - + -
394B ALA* 4.1 18.6 - - + -
395B ALA* 4.3 25.1 - - + -
398B TYR* 4.5 11.9 - + + -
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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