Contacts of the helix formed by residues 339 - 351 (chain B) in PDB entry 3V4K
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 339 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337B ILE 3.8 8.5 - - - +
338B MET* 1.3 73.7 - - - +
340B TYR* 1.3 69.4 + - - +
341B SER* 3.8 7.3 + - - -
342B GLU* 2.5 38.1 + - - +
343B PHE* 3.0 18.6 + - - -
364B LEU* 4.3 0.2 - - - -
365B ASP* 4.9 8.7 - - - +
368B SER* 3.3 22.0 - - - +
372B SER* 5.4 3.6 - - - +
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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
----------------------------------------------------------
339A THR* 5.0 6.1 - - - +
340A TYR* 3.6 45.9 - + + +
341A SER* 3.5 22.1 + - - +
365A ASP* 2.5 41.6 + - - -
339B THR* 1.3 76.1 - - - +
341B SER* 1.3 68.5 + - - +
343B PHE* 3.2 4.2 + - - +
344B LYS* 2.9 34.3 + - + +
358B PHE* 3.6 36.6 + + - -
360B PRO* 3.7 19.4 - - + +
364B LEU* 3.7 20.7 - - + +
365B ASP* 5.4 1.0 + - - -
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A THR* 4.1 22.3 + - - +
339B THR* 3.2 6.0 + - - -
340B TYR* 1.3 87.3 - - - +
342B GLU* 1.3 67.7 + - - +
344B LYS* 3.5 6.4 + - - +
345B HIS* 2.9 28.3 + - - +
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 4.2 9.4 - - + -
310B LYS* 4.1 30.9 + - + +
337B ILE 4.3 2.6 - - - +
338B MET* 3.8 20.9 - - + -
339B THR* 2.5 54.4 + - - +
341B SER* 1.3 82.7 - - - +
343B PHE* 1.3 64.8 + - - +
345B HIS* 3.3 6.2 + - - +
346B CYS* 3.0 28.8 + - - -
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Residues in contact with PHE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PHE* 3.8 6.3 - + + -
206B PHE* 3.3 35.0 - + + -
208B ASN* 3.9 22.7 - - + -
312B ALA* 3.9 18.4 - - + -
338B MET* 3.6 46.4 - - + -
339B THR 3.0 26.4 + - - -
340B TYR 3.7 2.9 - - - +
342B GLU* 1.3 74.6 - - - +
344B LYS* 1.3 63.1 + - - +
346B CYS* 3.2 4.0 + - - +
347B TRP* 2.9 23.9 + - - +
358B PHE* 3.7 22.2 - - + -
361B TRP* 3.7 18.8 - + - -
364B LEU* 3.9 17.3 - - + -
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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
----------------------------------------------------------
365A ASP* 2.8 47.4 + - + +
366A GLU* 5.5 0.9 - - - +
340B TYR* 2.9 23.7 + - + +
341B SER* 3.8 6.7 - - - +
343B PHE* 1.3 76.2 - - - +
345B HIS* 1.3 58.9 + - - +
347B TRP* 3.3 1.9 + - - +
348B ASP* 2.9 51.4 + - - +
357B PRO* 5.7 4.2 - - - +
358B PHE* 3.8 37.3 + - + +
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Residues in contact with HIS 345 (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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223B GLU* 3.0 29.4 + - - -
234B LYS* 4.0 15.7 - - - -
282B PHE* 3.7 28.3 - + - -
341B SER 2.9 18.3 + - - +
342B GLU* 3.6 6.7 - - - +
344B LYS* 1.3 78.2 - - - +
346B CYS* 1.3 60.1 + - - +
348B ASP* 3.3 6.1 + - - +
349B THR* 2.7 57.6 + - + -
350B PHE* 4.9 0.4 - + - -
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Residues in contact with CYS 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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202B PHE* 3.9 18.3 - - + -
206B PHE* 5.3 1.3 - - + -
221B CYS* 4.8 4.9 - - - -
282B PHE* 3.2 54.5 - - - -
338B MET* 3.8 7.4 - - + -
342B GLU 3.0 16.0 + - - +
343B PHE 3.7 4.0 - - - +
345B HIS* 1.3 75.5 - - - +
347B TRP* 1.3 59.8 + - - +
350B PHE* 2.9 47.2 + - + +
351B VAL* 3.7 2.3 + - - +
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Residues in contact with TRP 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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199B PRO* 3.8 26.9 - - + -
202B PHE* 3.6 31.2 - + + -
203B THR* 4.2 11.4 - - - -
343B PHE 2.9 14.0 + - - +
344B LYS 3.5 6.7 - - - +
346B CYS* 1.3 77.3 - - - +
348B ASP* 1.3 79.7 + - - +
351B VAL* 3.2 45.6 + - + +
353B HIS* 3.4 30.1 - + + +
356B ALA* 2.9 32.4 + - + -
357B PRO 3.9 11.7 - - - -
358B PHE* 3.3 33.7 - + + +
359B GLN* 5.8 3.8 - - + -
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Residues in contact with ASP 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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344B LYS* 2.9 48.4 + - - +
345B HIS* 3.7 6.6 - - - +
347B TRP* 1.3 93.1 - - - +
349B THR* 1.3 61.6 + - - +
351B VAL 4.8 0.5 - - - +
353B HIS* 3.2 25.9 + - - +
356B ALA 5.3 0.7 - - - +
357B PRO* 5.4 1.7 - - - +
358B PHE 4.7 2.6 + - - -
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Residues in contact with THR 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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196B SER* 5.4 1.7 + - - -
223B GLU* 4.2 10.3 - - - +
239B ARG* 5.6 5.4 - - + -
345B HIS* 2.7 41.4 + - + +
348B ASP* 1.3 80.5 - - - +
350B PHE* 1.3 91.8 + - + +
351B VAL 3.8 1.1 - - - -
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Residues in contact with PHE 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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195B HIS 4.6 2.6 - - - +
196B SER* 3.5 10.7 - - - +
197B MET* 2.8 30.0 + - + +
202B PHE* 6.2 0.2 - - + -
221B CYS* 3.6 39.0 - - + -
222B TYR 3.4 23.6 - - - -
223B GLU* 4.0 11.9 - - + -
239B ARG* 4.3 6.1 - - + -
240B GLY* 3.4 37.7 - - - -
241B PHE* 4.5 5.3 - + + -
282B PHE* 4.1 15.3 - + - -
345B HIS* 4.8 1.1 - - - -
346B CYS* 2.9 24.3 + - - +
349B THR* 1.3 103.4 - - + +
351B VAL* 1.3 63.5 + - + +
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B SER* 4.1 5.5 + - - -
197B MET* 3.5 16.6 - - + +
199B PRO* 3.8 29.6 - - + -
202B PHE* 3.5 39.0 - - + -
346B CYS 3.9 1.3 - - - +
347B TRP* 3.2 40.2 + - + +
348B ASP 4.8 0.5 - - - +
349B THR 5.2 0.7 - - - -
350B PHE* 1.3 81.1 + - + +
352B ASP* 1.3 62.9 + - - +
353B HIS* 2.8 26.5 + - - +
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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