Contacts of the helix formed by residues 339 - 353 (chain B) in PDB entry 6HBU
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 SER 339 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B TYR* 3.2 30.7 - - - -
335B ILE* 3.1 13.7 + - - -
336B TYR* 3.1 18.7 + - - -
337B VAL 3.2 2.1 - - - +
338B ASN* 1.3 77.2 - - - +
340B SER* 1.3 68.9 + - - +
341B PHE* 3.4 12.6 + - - -
342B TYR 4.1 1.7 + - - -
343B LYS* 3.0 30.5 + - - +
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Residues in contact with SER 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B SER* 1.3 79.1 + - - +
341B PHE* 1.3 62.5 + - - -
342B TYR 3.2 2.2 - - - -
343B LYS* 3.3 11.8 + - - +
344B GLU* 3.0 42.8 + - - +
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Residues in contact with PHE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PHE* 3.7 15.0 - + - -
267B HIS 3.8 15.4 - - - +
268B GLY* 4.5 0.7 - - - -
269B PRO* 4.0 20.9 - - + -
272B GLU* 3.4 44.2 - - + -
276B TYR* 3.6 36.3 - + + -
336B TYR* 3.8 14.7 + - + -
339B SER* 3.4 6.2 + - - +
340B SER* 1.3 79.4 - - - +
342B TYR* 1.3 59.2 + - - +
344B GLU* 3.9 18.9 + - - +
345B THR* 2.9 26.3 + - - -
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Residues in contact with TYR 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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68B ASN* 3.5 33.2 + - + -
264B LEU* 5.8 1.6 - - + -
336B TYR* 3.2 49.1 + + + +
337B VAL* 3.3 45.8 - - + +
339B SER 4.1 2.3 + - - +
340B SER 3.2 0.4 - - - -
341B PHE* 1.3 78.6 - - - +
343B LYS* 1.3 63.9 + - + +
344B GLU 3.3 0.2 - - - -
345B THR* 3.3 5.6 + - + -
346B LYS* 3.0 56.6 + - + +
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B VAL 4.4 5.1 + - - +
338B ASN* 3.0 33.3 + - - +
339B SER 3.0 14.5 + - - +
340B SER* 3.3 13.1 + - - +
342B TYR* 1.3 79.6 - - + +
344B GLU* 1.3 63.3 + - + +
346B LYS* 4.5 4.2 - - - +
347B ALA* 3.2 26.0 + - - +
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Residues in contact with GLU 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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269B PRO* 5.8 1.6 - - - +
272B GLU* 5.7 0.2 - - - +
340B SER* 3.0 32.0 + - - +
341B PHE* 4.1 21.0 - - - +
342B TYR 3.3 0.2 - - - -
343B LYS* 1.3 77.2 - - - +
345B THR* 1.3 62.4 + - - +
347B ALA* 4.2 3.9 - - - +
348B GLU* 3.6 19.2 + - - +
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Residues in contact with THR 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASN* 4.4 7.2 - - + +
69B GLY* 4.0 23.1 - - - +
70B ILE* 4.0 14.2 - - + +
267B HIS* 4.2 15.2 + - + -
336B TYR* 4.3 3.1 + - - +
341B PHE 2.9 18.4 + - - -
342B TYR* 3.3 9.9 + - + -
344B GLU* 1.3 77.8 - - - +
346B LYS* 1.3 62.6 + - - +
348B GLU* 3.1 4.5 + - - +
349B LEU* 2.8 46.5 + - + +
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Residues in contact with LYS 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B HIS* 3.1 26.7 + - - -
41B ASN* 3.9 9.7 + - - +
68B ASN* 3.4 33.6 - - + +
342B TYR* 3.0 52.5 + - + +
343B LYS* 4.5 3.4 - - - +
345B THR* 1.3 75.9 - - - +
347B ALA* 1.3 59.6 + - - +
349B LEU* 4.1 10.3 - - + -
350B HIS* 2.5 50.9 + - + -
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Residues in contact with ALA 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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343B LYS 3.2 19.6 + - - +
344B GLU* 4.2 5.8 - - - +
345B THR 3.2 0.8 - - - -
346B LYS* 1.3 77.1 - - - +
348B GLU* 1.3 58.6 + - - +
350B HIS* 4.4 4.3 - - - +
351B GLN* 3.8 18.4 + - - +
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Residues in contact with GLU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 3.7 24.7 - - + -
72B LYS* 5.1 14.3 + - - +
344B GLU 3.6 10.8 + - - +
345B THR 3.1 3.6 + - - +
347B ALA* 1.3 78.0 - - - +
349B LEU* 1.3 58.5 + - - +
350B HIS 3.3 1.8 - - - -
351B GLN* 2.9 31.9 + - - +
352B LEU* 2.9 46.7 + - + +
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Residues in contact with LEU 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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38B SER* 3.9 15.0 - - - +
39B PHE 3.9 6.5 - - - +
40B HIS* 3.9 36.3 + - + +
68B ASN* 3.7 29.2 - - + -
69B GLY 3.7 22.2 - - - +
70B ILE* 3.7 12.1 - - + -
345B THR* 2.8 32.0 + - + +
346B LYS* 4.1 11.4 - - + +
348B GLU* 1.3 77.1 - - - +
350B HIS* 1.3 57.2 + - - +
352B LEU* 3.6 3.7 + - - +
353B SER* 3.1 29.8 + - - -
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Residues in contact with HIS 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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40B HIS* 4.0 21.6 + + - -
346B LYS* 2.5 58.6 + - + +
347B ALA* 4.8 3.6 - - - +
348B GLU 3.3 0.4 - - - -
349B LEU* 1.3 76.1 - - + +
351B GLN* 1.3 61.0 + - - +
353B SER* 4.0 17.2 + - - +
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Residues in contact with GLN 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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347B ALA 3.8 15.0 + - - +
348B GLU* 2.9 37.8 + - - +
350B HIS* 1.3 78.2 - - - +
352B LEU* 1.3 64.7 + - + +
353B SER 4.5 1.7 - - - -
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Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 4.5 21.1 - - + +
38B SER* 3.8 31.0 - - - +
70B ILE* 4.5 13.5 - - + -
72B LYS* 6.2 0.2 - - - +
107B LEU* 5.0 1.3 - - + -
109B ASN* 5.1 3.1 - - - -
110B GLY* 3.8 39.2 - - - +
348B GLU* 2.9 35.8 + - + +
349B LEU* 4.0 5.2 - - + +
351B GLN* 1.3 78.5 - - + +
353B SER* 1.3 62.8 + - - +
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Residues in contact with SER 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B HIS* 5.0 12.2 + - - -
105B ASP* 5.0 7.1 + - - -
107B LEU* 4.4 19.9 - - - +
110B GLY 5.1 0.7 - - - -
349B LEU 3.1 19.1 + - - -
350B HIS* 4.0 15.3 - - - +
351B GLN 3.5 2.7 - - - -
352B LEU* 1.3 81.3 - - - +
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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