Contacts of the helix formed by residues 331 - 344 (chain B) in PDB entry 4EUT
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 331 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B ILE* 4.0 6.2 - - - +
329B TYR 4.8 1.6 - - - +
330B ASN* 1.3 77.6 - - - +
332B ALA* 1.3 63.9 + - - +
333B THR* 3.3 11.0 + - - -
334B ILE* 3.2 30.7 + - + +
335B PHE* 3.3 14.2 + - - +
363B PRO 3.6 13.0 - - - +
364B GLY* 4.5 8.3 - - - -
365B ARG 3.4 9.4 - - - -
366B LEU* 4.4 9.0 - - + -
370B PHE* 4.8 1.9 - - - -
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B THR* 1.3 72.0 - - - +
333B THR* 1.3 68.1 + - - +
335B PHE* 2.8 13.9 + - - +
336B HIS* 2.9 21.5 + - + -
361B LEU* 4.0 17.0 - - + +
362B GLU 3.2 27.1 - - - +
363B PRO* 3.6 4.5 + - + +
365B ARG* 3.2 9.4 + - + +
370B PHE* 3.9 25.8 - - + -
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Residues in contact with THR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B THR* 3.3 9.7 + - - -
332B ALA* 1.3 80.0 - - - +
334B ILE* 1.3 63.3 + - + +
336B HIS* 3.3 11.7 + - - +
337B GLU* 3.2 19.8 + - + +
347B SER* 5.7 0.7 - - - -
363B PRO* 2.9 26.6 + - - +
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ILE* 4.4 1.1 - - + -
330B ASN* 3.7 45.1 - - + +
331B THR* 3.2 23.8 + - + +
332B ALA 3.1 0.6 - - - -
333B THR* 1.3 79.7 - - + +
335B PHE* 1.3 66.9 + - - +
337B GLU* 2.9 22.1 + - - +
338B LEU* 2.9 38.4 + - + +
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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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311B ILE* 3.7 44.9 - - + -
313B VAL* 3.7 27.1 - - + -
324B ILE* 4.1 14.1 - - + -
326B ILE* 4.2 10.3 - - + +
331B THR 3.3 7.0 + - - +
332B ALA 2.8 17.2 + - - +
334B ILE* 1.3 73.9 - - - +
336B HIS* 1.3 68.6 + - - +
338B LEU* 3.0 9.0 + - - +
339B VAL* 2.9 43.2 + - + +
352B LEU* 4.1 24.5 - - + -
361B LEU* 4.3 8.3 - - + -
370B PHE* 3.8 20.4 - + + -
379B ILE* 4.6 11.4 - - + -
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Residues in contact with HIS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ALA* 2.9 29.9 + - + -
333B THR* 3.6 9.6 - - - +
335B PHE* 1.3 83.7 - + - +
337B GLU* 1.3 57.6 + - - +
339B VAL* 3.2 1.9 + - - -
340B TYR* 2.9 24.8 + - - +
347B SER* 3.9 22.2 - - - -
350B GLN* 2.7 46.7 + - + +
352B LEU* 4.0 31.2 - - + -
361B LEU* 4.3 20.2 + - - +
363B PRO* 6.4 0.7 - - + -
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Residues in contact with GLU 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 THR* 3.2 12.7 + - + +
334B ILE* 2.9 25.3 + - - +
336B HIS* 1.3 72.8 - - - +
338B LEU* 1.3 62.7 + - - +
340B TYR* 3.3 13.1 + - + +
341B LYS* 3.1 52.6 + - + +
347B SER* 5.1 3.3 - - - -
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Residues in contact with LEU 338 (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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308B ARG* 4.7 6.1 - - - +
324B ILE* 3.6 32.7 - - + +
325B TYR 3.5 26.0 - - - +
326B ILE* 4.2 10.3 - - + -
334B ILE* 2.9 31.4 + - + +
335B PHE 3.5 7.4 - - - +
337B GLU* 1.3 78.7 - - + +
339B VAL* 1.3 60.4 + - - +
341B LYS* 3.5 32.5 + - + +
342B GLN* 3.6 17.7 + - - +
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B VAL* 4.6 7.4 - - + -
324B ILE* 4.1 15.3 - - + -
335B PHE* 2.9 52.5 + - + +
336B HIS* 3.4 8.7 - - - +
337B GLU 3.2 0.2 - - - -
338B LEU* 1.3 75.8 - - - +
340B TYR* 1.3 54.1 + - - +
342B GLN* 3.4 1.8 + - - +
343B THR* 2.4 57.8 + - + +
350B GLN* 3.4 24.7 - - + +
352B LEU* 6.0 1.3 - - + -
381B VAL* 4.5 14.6 - - + -
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Residues in contact with TYR 340 (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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336B HIS 2.9 14.3 + - - +
337B GLU* 3.7 15.5 - - + +
339B VAL* 1.3 77.7 - - - +
341B LYS* 1.3 71.2 + - + +
343B THR* 3.2 7.2 - - - -
344B LYS* 2.6 57.2 + - + +
345B ILE 3.3 25.6 - - - +
346B ILE* 4.1 20.9 - - + +
347B SER* 4.6 5.4 - - - +
350B GLN* 3.4 0.9 - - - +
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Residues in contact with LYS 341 (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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337B GLU* 3.1 39.7 + - + +
338B LEU* 3.6 28.2 - - + +
339B VAL 3.3 0.2 - - - -
340B TYR* 1.3 89.4 - - + +
342B GLN* 1.3 60.6 + - + +
344B LYS* 3.6 19.4 + - - +
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Residues in contact with GLN 342 (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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271B ARG* 4.1 19.5 - - + +
272B GLY* 3.4 28.7 + - - -
275B VAL* 6.2 1.6 - - + -
318B GLN* 5.2 0.5 + - - -
322B HIS* 3.3 40.9 + - + +
323B LYS 3.2 21.9 + - - +
324B ILE* 3.6 20.9 - - + +
325B TYR 5.2 0.4 - - - +
338B LEU* 3.6 12.1 + - - +
339B VAL 3.4 4.7 + - - +
340B TYR 3.1 0.2 - - - -
341B LYS* 1.3 83.7 - - + +
343B THR* 1.3 64.9 + - + +
344B LYS* 3.5 7.7 - - - +
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Residues in contact with THR 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B VAL* 5.5 1.6 - - + -
315B SER* 4.7 4.7 - - - +
318B GLN* 2.7 37.3 + - - +
322B HIS* 4.8 12.6 - - + +
324B ILE* 6.4 0.2 - - + -
339B VAL* 2.4 59.9 + - + +
340B TYR* 3.2 0.7 - - - -
342B GLN* 1.3 75.3 - - + +
344B LYS* 1.3 75.7 + - - +
345B ILE* 2.9 29.8 + - + +
381B VAL* 4.3 16.6 - - + -
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Residues in contact with LYS 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLN* 5.0 0.9 - - - +
340B TYR* 2.6 47.2 + - + +
341B LYS* 3.6 23.5 + - - +
342B GLN 4.2 6.1 - - - +
343B THR* 1.3 78.5 - - - +
345B ILE* 1.3 60.2 + - - +
346B ILE* 4.0 3.3 + - - +
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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