Contacts of the helix formed by residues 342 - 353 (chain B) in PDB entry 2AJH
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 ASP 342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338B VAL 3.4 1.3 + - - +
339B PRO 3.9 0.7 - - - +
341B HIS* 1.3 78.2 - - - +
343B GLN* 1.3 61.3 + - - +
344B ARG* 3.0 16.7 + - - +
345B ASP* 2.6 54.2 + - + +
346B TYR* 2.7 28.2 + - - +
374B ALA* 3.8 3.4 - - - +
376B THR* 4.6 1.8 - - - -
601B MET* 3.6 32.7 + - + +
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Residues in contact with GLN 343 (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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369A ASP* 5.1 3.6 - - - +
372A GLN* 4.3 12.4 + - - +
342B ASP* 1.3 73.6 + - - +
344B ARG* 1.3 61.3 + - - +
346B TYR* 3.2 10.7 + - - +
347B GLU* 2.8 65.5 + - - +
372B GLN 5.4 0.4 + - - -
373B GLN* 3.4 17.0 - - - +
374B ALA* 3.2 32.6 + - - +
376B THR* 4.2 15.9 - - + +
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Residues in contact with ARG 344 (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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362A ALA* 5.4 2.2 - - - +
364A ASP* 2.9 30.1 + - - -
366A SER* 2.9 17.8 + - - -
367A GLU 4.0 11.1 + - - -
369A ASP* 4.0 25.8 + - + +
300B LYS* 3.8 32.4 - - + +
325B PHE* 3.3 47.9 - - + -
335B VAL* 4.8 4.0 - - - +
342B ASP* 3.0 10.9 + - - +
343B GLN* 1.3 72.5 - - - +
345B ASP* 1.3 96.9 + - - +
347B GLU* 3.4 2.9 + - - +
348B PHE* 3.2 22.0 + - - +
601B MET 4.4 4.6 + - - -
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Residues in contact with ASP 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B TYR* 2.9 22.3 + - - +
335B VAL* 5.4 0.5 - - - +
337B ALA* 3.1 18.0 - - - +
338B VAL 2.9 14.1 + - - +
339B PRO* 3.5 22.0 - - + +
342B ASP* 2.6 31.4 + - + +
344B ARG* 1.3 104.4 + - - +
346B TYR* 1.3 61.8 + - - +
348B PHE 3.2 1.4 + - - -
349B ALA 3.1 11.6 + - - -
601B MET 2.8 26.4 + - - -
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Residues in contact with TYR 346 (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 PRO* 3.1 30.2 - - - +
340B GLY* 5.1 0.4 - - - -
342B ASP 2.7 14.0 + - - +
343B GLN* 3.2 18.6 + - - +
345B ASP* 1.3 72.2 - - - +
347B GLU* 1.3 62.4 + - + +
349B ALA* 3.2 5.2 + - - +
350B SER* 3.0 49.8 + - - -
356B ILE* 4.1 21.4 - - + +
370B LEU* 2.7 28.7 + - + -
371B SER 3.4 8.0 + - - -
372B GLN 3.2 25.3 + - - -
373B GLN* 3.2 20.0 - - - -
374B ALA* 3.1 22.9 - - + -
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Residues in contact with GLU 347 (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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369A ASP* 4.3 3.2 - - - +
371A SER* 4.6 5.2 + - - -
372A GLN* 3.6 18.1 + - - +
300B LYS* 3.1 32.7 + - + +
343B GLN* 2.8 52.6 + - - +
344B ARG 3.9 4.0 - - - +
345B ASP 3.3 0.2 - - - -
346B TYR* 1.3 82.6 - - + +
348B PHE* 1.3 58.0 + - - +
350B SER* 3.7 5.7 - - - -
351B LYS* 3.1 28.1 + - - +
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Residues in contact with PHE 348 (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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258B TYR* 3.1 42.4 - + - +
260B ALA* 5.5 0.2 - - + -
300B LYS* 4.4 14.8 - - + +
301B LYS 3.5 24.2 - - - -
302B GLY* 4.3 3.8 - - - -
321B TRP* 3.8 38.4 - + + -
322B ALA 4.3 2.7 - - - -
323B ALA* 4.2 6.1 - - + -
325B PHE* 3.6 28.0 - + + -
344B ARG 3.2 17.2 + - - +
347B GLU* 1.3 76.2 - - - +
349B ALA* 1.3 63.7 + - - +
351B LYS* 3.5 2.8 + - - -
352B TYR* 3.2 43.0 + + - +
354B LEU* 4.2 8.7 - - + -
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Residues in contact with ALA 349 (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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258B TYR* 4.1 2.5 - - + -
339B PRO* 3.6 26.7 - - + -
345B ASP 3.1 6.0 + - - +
346B TYR 3.5 8.3 - - - +
348B PHE* 1.3 76.7 - - - +
350B SER* 1.3 55.2 + - - +
352B TYR 3.0 1.0 + - - -
353B GLY* 2.6 33.6 + - - -
354B LEU* 3.1 44.6 + - + +
356B ILE* 3.8 5.6 - - + -
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Residues in contact with SER 350 (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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346B TYR* 3.0 42.0 + - - -
347B GLU* 3.7 8.7 - - - -
349B ALA* 1.3 77.1 - - - +
351B LYS* 1.3 61.5 + - - +
352B TYR 3.4 0.5 + - - -
353B GLY* 3.9 5.7 + - - -
356B ILE* 3.8 10.5 - - - +
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Residues in contact with LYS 351 (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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299B GLU* 2.9 28.8 + - - +
300B LYS* 3.4 17.8 + - + +
301B LYS* 4.1 9.3 - - - +
347B GLU 3.1 16.2 + - - +
348B PHE* 3.5 3.3 + - - +
349B ALA 3.3 0.2 - - - -
350B SER* 1.3 80.1 - - - +
352B TYR* 1.3 101.4 + - + +
353B GLY 3.6 0.2 - - - -
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Residues in contact with TYR 352 (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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301B LYS* 3.3 16.2 + - - +
302B GLY* 2.8 44.7 + - - -
321B TRP* 3.4 36.4 - + + -
348B PHE* 3.2 45.7 + + + +
349B ALA 3.0 2.9 + - - +
351B LYS* 1.3 118.4 + - + +
353B GLY* 1.3 63.8 + - - +
354B LEU* 3.9 11.7 - - + +
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Residues in contact with GLY 353 (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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349B ALA 2.6 12.3 + - - -
350B SER 3.9 5.0 + - - -
351B LYS 3.6 2.2 - - - -
352B TYR* 1.3 74.9 - - - +
354B LEU* 1.3 63.6 + - - +
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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