Contacts of the helix formed by residues 324 - 336 (chain B) in PDB entry 3H60
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 THR 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B ARG* 6.2 4.0 - - - -
319B VAL 3.4 4.8 + - - +
320B LYS* 4.3 9.4 - - - +
323B TYR* 1.3 91.9 - - + +
325B ALA* 1.3 63.2 + - - +
326B GLN* 3.4 12.6 + - - +
327B MET* 3.1 20.1 + - - +
328B TYR* 3.1 20.3 + - - +
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Residues in contact with ALA 325 (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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320B LYS* 4.1 29.5 - - + +
324B THR* 1.3 73.1 - - - +
326B GLN* 1.3 65.3 + - + +
328B TYR* 3.1 3.5 + - - -
329B GLU* 3.0 36.5 + - - +
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Residues in contact with GLN 326 (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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324B THR* 3.2 10.6 + - - +
325B ALA* 1.3 80.9 - - + +
327B MET* 1.3 60.6 + - - +
329B GLU* 3.5 9.6 + - + +
330B LEU* 3.1 21.7 + - - +
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Residues in contact with MET 327 (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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206B ARG* 3.5 31.2 - - + +
209B ALA* 3.7 17.0 - - + -
210B TYR* 4.0 11.7 - - + +
213B LEU* 3.8 22.7 - - - -
319B VAL* 3.9 9.4 - - + -
323B TYR* 3.7 41.5 - - + -
324B THR* 3.1 18.5 + - - +
325B ALA 3.2 0.2 - - - -
326B GLN* 1.3 73.8 - - - +
328B TYR* 1.3 66.6 + - - +
330B LEU* 3.2 10.9 + - - +
331B PHE* 3.1 28.6 + - + -
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Residues in contact with TYR 328 (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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307B ASP* 3.5 16.6 + - - -
310B ASN* 2.8 42.1 + - + +
311B GLN* 3.4 24.4 + - - -
315B PHE* 3.9 11.4 - + - -
316B GLU* 3.7 47.8 - - + +
319B VAL* 3.5 26.1 - - + +
320B LYS* 4.7 2.5 - - + -
324B THR 3.1 10.2 + - - +
325B ALA* 3.1 11.0 + - - +
327B MET* 1.3 77.1 - - - +
329B GLU* 1.3 81.3 + - - +
331B PHE* 3.1 5.5 + - + +
332B SER* 3.0 23.6 + - - -
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Residues in contact with GLU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ASP* 5.7 1.0 - - - +
316B GLU* 5.1 0.9 - - - +
320B LYS* 4.9 4.5 + - - -
325B ALA* 3.0 33.9 + - + +
326B GLN* 3.5 8.3 + - + +
327B MET 3.3 0.2 - - - -
328B TYR* 1.3 90.1 - - - +
330B LEU* 1.3 63.4 + - - +
332B SER* 3.4 10.4 - - - -
333B GLU* 3.1 35.2 + - - +
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Residues in contact with LEU 330 (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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210B TYR* 3.7 33.0 - - + -
213B LEU* 3.6 32.8 - - + -
214B VAL* 4.1 14.8 - - + -
217B LYS* 5.0 7.2 - - + -
326B GLN 3.1 14.2 + - - +
327B MET* 3.2 15.0 + - - +
329B GLU* 1.3 73.9 - - - +
331B PHE* 1.3 66.2 + - - +
333B GLU* 3.1 21.2 + - + +
334B VAL* 3.0 35.9 + - + +
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Residues in contact with PHE 331 (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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209B ALA* 6.0 0.4 - - + -
213B LEU* 3.4 38.3 - - + +
280B VAL* 5.0 5.8 - - + -
283B ILE* 3.5 29.6 - - + -
284B LEU* 3.9 19.3 - - + -
287B PHE* 4.1 11.4 - + - -
315B PHE* 3.9 21.3 - + + -
319B VAL* 3.8 35.2 - - + -
323B TYR* 5.1 3.6 - + - -
327B MET* 3.1 30.0 + - + -
328B TYR* 3.1 7.8 + - + +
330B LEU* 1.3 72.8 - - - +
332B SER* 1.3 63.8 + - - +
334B VAL* 3.0 6.7 + - - +
335B PHE* 2.8 37.0 + + + -
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Residues in contact with SER 332 (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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307B ASP* 2.7 36.6 + - - -
328B TYR* 3.0 21.0 + - - -
329B GLU* 3.4 16.6 - - - -
331B PHE* 1.3 77.0 - - - +
333B GLU* 1.3 62.7 + - - +
335B PHE* 3.3 12.9 + - - +
336B GLU* 3.2 26.7 + - - +
374B GLN* 3.9 7.5 + - - +
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Residues in contact with GLU 333 (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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217B LYS* 3.5 28.2 + - - +
329B GLU* 3.1 22.7 + - - +
330B LEU* 3.1 19.9 + - - +
332B SER* 1.3 74.6 - - - +
334B VAL* 1.3 64.2 + - - +
336B GLU* 3.5 27.8 - - - +
337B TRP* 3.6 15.6 - - - -
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Residues in contact with VAL 334 (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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213B LEU* 3.8 35.0 - - + +
216B VAL* 3.5 28.9 - - + -
217B LYS* 3.8 20.2 - - + +
220B LEU* 3.8 10.9 - - + +
287B PHE* 3.7 18.2 - - + -
330B LEU* 3.0 21.0 + - + +
331B PHE 3.0 7.4 + - - +
333B GLU* 1.3 75.9 - - - +
335B PHE* 1.3 64.0 + - - +
337B TRP* 3.1 17.7 + - - +
338B LEU 3.8 3.5 + - - -
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Residues in contact with PHE 335 (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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273B VAL* 4.3 8.5 - - + -
283B ILE* 3.8 22.7 - - + -
287B PHE* 3.7 27.4 - + - -
301B ARG* 3.5 13.0 + - - +
305B GLU* 3.6 53.8 - - + +
306B THR* 5.2 0.7 - - - -
310B ASN* 3.7 14.1 - - - -
315B PHE* 3.7 33.7 - + - -
331B PHE* 2.8 23.7 + + + -
332B SER* 3.3 12.1 + - - +
334B VAL* 1.3 76.9 - - - +
336B GLU* 1.3 55.2 + - - +
338B LEU* 3.0 37.8 + - + +
374B GLN* 6.0 0.4 - - - +
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Residues in contact with GLU 336 (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 ARG* 3.7 9.9 + - - +
307B ASP* 5.2 0.3 - - - +
332B SER* 3.2 15.7 + - - +
333B GLU* 3.5 23.7 - - - +
334B VAL 3.2 0.2 - - - -
335B PHE* 1.3 78.1 - - - +
337B TRP* 1.3 62.2 + - + +
338B LEU 3.8 0.9 + - - +
371B ARG* 3.2 25.6 - - - +
372B ASN* 3.3 19.9 - - + +
373B ARG* 3.6 25.9 - - - +
374B GLN* 2.9 34.9 + - - +
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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