Contacts of the helix formed by residues 325 - 337 (chain B) in PDB entry 1TUB
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 MET 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A TYR* 4.3 0.7 + - - -
223A THR* 3.3 6.6 - - - +
224A TYR* 2.6 62.5 - - + +
247B GLN* 3.1 57.7 - - + +
248B LEU* 3.8 8.5 - - + +
323B MET 3.3 5.6 + - - +
324B SER* 1.4 74.0 - - - +
326B LYS* 1.2 57.4 + - - +
328B VAL* 4.4 2.7 - - - -
329B ASP* 3.1 32.3 - - - +
355B VAL* 3.5 39.0 - - + -
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Residues in contact with LYS 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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210A TYR* 1.8 59.0 - - + -
213A CYS* 3.4 26.9 - - - +
222A PRO* 2.6 53.3 + - + +
223A THR 3.0 19.0 + - - -
226A ASN* 3.8 6.7 - - - +
227A LEU* 3.2 25.3 - - - +
325B MET* 1.2 80.9 - - - +
327B GLU* 1.3 52.7 + - - -
328B VAL 3.5 0.2 - - - -
329B ASP* 4.9 1.6 - - - -
330B GLU* 2.3 47.4 + - - +
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLU 3.6 6.4 - - - +
221A ARG* 3.4 27.0 + - - +
222A PRO 3.4 0.2 + - - -
288B VAL* 3.6 1.1 - - + +
289B PRO* 5.3 2.4 - - - +
323B MET* 1.7 45.4 - - + +
324B SER* 1.5 45.0 + - - +
326B LYS* 1.3 72.6 - - - +
328B VAL* 1.3 56.2 + - - +
330B GLU* 4.1 6.2 - - - +
331B GLN* 2.6 54.7 + - - +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B VAL* 4.1 8.3 - - + -
319B PHE* 2.2 73.6 - - + +
323B MET* 4.6 18.2 - - + +
324B SER 3.1 18.5 + - - +
325B MET 5.1 0.4 - - - +
326B LYS 3.5 0.2 - - - -
327B GLU* 1.3 74.0 - - - +
329B ASP* 1.4 64.1 + - - +
331B GLN* 3.0 9.2 + - - +
332B MET* 2.9 23.7 + - - +
353B THR* 3.3 4.9 - - + -
355B VAL* 4.2 13.5 - - + -
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Residues in contact with ASP 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLN* 3.0 22.4 - - + +
177A VAL* 5.3 10.1 - - - +
178A SER* 4.8 5.7 + - - -
210A TYR* 5.8 0.9 - - + -
224A TYR* 3.2 25.3 + - - -
248B LEU* 6.0 0.5 - - - +
325B MET* 3.1 24.9 - - - +
326B LYS* 3.7 3.5 + - - +
328B VAL* 1.4 75.2 - - - +
330B GLU* 1.3 70.1 + - + +
331B GLN 3.2 0.5 + - - -
332B MET* 3.7 12.6 + - - +
333B LEU 3.9 3.3 + - - -
353B THR* 3.5 27.9 - - - +
355B VAL* 5.4 1.7 - - - +
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLN* 3.8 11.3 + - - +
207A GLU* 6.1 0.4 - - - +
210A TYR* 3.5 27.3 - - + +
214A ARG* 5.9 6.3 - - - -
220A GLU* 3.4 22.9 - - - +
222A PRO* 4.1 1.4 - - - +
326B LYS* 2.3 44.2 + - - +
327B GLU* 4.0 9.4 - - - +
329B ASP* 1.3 79.9 - - + +
331B GLN* 1.4 73.5 + - - +
333B LEU* 3.6 13.0 - - - +
334B ASN* 3.5 11.3 + - - -
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B VAL* 3.6 16.8 - - + -
289B PRO* 4.0 20.3 - - - +
292B THR* 3.7 26.8 + - + +
327B GLU* 2.6 40.6 + - - +
328B VAL 3.0 5.4 + - - +
330B GLU* 1.4 89.0 + - - +
332B MET* 1.1 68.9 + - - +
333B LEU 3.0 4.0 + - - -
334B ASN* 3.7 24.3 + - - +
335B VAL* 3.9 7.1 - - - +
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Residues in contact with MET 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B THR* 3.4 15.7 - - - -
295B MET* 5.1 2.7 - - - -
296B PHE* 3.5 32.3 - - + -
317B ALA* 3.6 27.4 - - + -
319B PHE* 3.0 33.2 - - + -
328B VAL 2.9 22.9 - - - +
329B ASP* 4.0 6.5 - - - +
331B GLN* 1.1 76.1 - - - +
333B LEU* 1.3 59.5 + - - +
334B ASN 3.3 0.4 - - - -
335B VAL* 3.4 12.9 - - - +
336B GLN* 3.0 26.3 + - - +
351B VAL* 3.9 17.8 - - + +
353B THR* 3.6 13.5 - - - +
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Residues in contact with LEU 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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175A PRO* 5.3 7.0 - - + +
176A GLN* 2.4 56.1 - - + +
207A GLU* 5.1 1.3 - - - +
329B ASP 3.9 1.8 + - - -
330B GLU 3.6 8.3 + - - +
331B GLN 3.0 0.6 - - - -
332B MET* 1.3 74.5 - - - +
334B ASN* 1.3 57.1 + - - +
335B VAL 3.0 1.3 - - - -
336B GLN* 2.7 44.4 + - + +
337B ASN* 2.7 42.6 + - - +
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Residues in contact with ASN 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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330B GLU 3.5 21.5 + - - -
331B GLN* 3.7 28.1 + - - +
333B LEU* 1.3 77.4 - - - +
335B VAL* 1.1 67.8 + - + +
337B ASN* 3.8 14.2 + - - +
338B LYS* 3.8 22.5 + - + +
339B ASN* 4.3 0.2 + - - -
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Residues in contact with VAL 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B THR* 4.1 13.0 - - - +
293B GLN* 5.9 0.7 - - - -
296B PHE* 2.8 67.3 - - + -
331B GLN 3.9 16.6 - - - +
332B MET* 3.4 10.3 - - - +
334B ASN* 1.1 81.1 - - + +
336B GLN* 1.3 60.6 + - + +
337B ASN 3.3 0.5 + - - -
339B ASN* 1.6 47.7 + - - +
343B PHE* 4.5 2.2 - - + -
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Residues in contact with GLN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PRO 5.6 1.2 - - - +
176A GLN* 5.6 1.8 - - - +
332B MET* 3.0 21.7 + - - +
333B LEU* 2.7 34.8 + - + +
335B VAL* 1.3 74.4 - - + +
337B ASN* 1.3 61.1 + - - +
339B ASN* 4.2 5.9 - - - -
340B SER* 4.1 14.0 + - - -
343B PHE* 4.6 17.9 - - + +
349B ASN* 5.9 1.1 - - - +
350B ASN* 4.9 8.4 + - + +
351B VAL* 2.9 53.0 + - + +
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Residues in contact with ASN 337 (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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333B LEU* 2.7 51.1 + - - +
334B ASN* 4.0 7.9 + - - +
335B VAL 3.1 1.2 - - - -
336B GLN* 1.3 82.6 - - - +
338B LYS* 1.2 67.3 + - + +
339B ASN 3.2 5.6 - - - -
340B SER* 4.4 6.9 + - - -
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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