Contacts of the helix formed by residues 339 - 353 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A TYR* 3.3 31.1 - - - -
335A ILE* 3.1 12.4 + - - -
336A TYR* 3.1 20.0 + - - -
337A VAL 4.0 1.6 - - - +
338A ASN* 1.3 78.0 - - - +
340A SER* 1.3 68.8 + - - +
341A PHE* 3.4 12.6 + - - -
342A TYR 4.1 1.5 + - - -
343A LYS* 3.0 29.5 + - - +
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Residues in contact with SER 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A SER* 1.3 78.7 + - - +
341A PHE* 1.3 61.8 + - - -
342A TYR 3.2 2.2 - - - -
343A LYS* 3.3 12.7 + - - +
344A GLU* 3.0 42.5 + - - +
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Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PHE* 3.7 13.9 - + - -
267A HIS 3.8 14.3 - - - +
268A GLY* 4.5 0.4 - - - -
269A PRO* 4.0 20.6 - - + -
272A GLU* 3.4 45.5 - - + -
276A TYR* 3.6 36.8 - + + -
336A TYR* 3.8 15.1 + - + -
339A SER* 3.4 6.2 + - - +
340A SER* 1.3 81.3 - - - +
342A TYR* 1.3 59.0 + - - +
344A GLU* 4.0 17.9 - - - +
345A THR* 2.9 26.7 + - - -
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Residues in contact with TYR 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN* 3.5 33.6 + - + -
264A LEU* 5.8 1.8 - - + -
336A TYR* 3.2 48.8 + + + +
337A VAL* 3.3 46.0 - - + +
339A SER 4.1 2.7 + - - +
340A SER 3.2 0.4 - - - -
341A PHE* 1.3 78.0 - - - +
343A LYS* 1.3 64.1 + - + +
344A GLU 3.3 0.4 - - - -
345A THR* 3.3 4.4 + - + +
346A LYS* 3.0 57.4 + - + +
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Residues in contact with LYS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A VAL 4.4 4.7 + - - +
338A ASN* 3.0 32.9 + - - +
339A SER 3.0 15.9 + - - +
340A SER* 3.3 13.3 + - - +
342A TYR* 1.3 80.5 - - + +
344A GLU* 1.3 63.6 + - + +
346A LYS* 4.5 2.9 - - - +
347A ALA* 3.2 26.2 + - - +
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A PRO* 5.8 1.6 - - - +
340A SER* 3.0 31.7 + - - +
341A PHE* 4.1 21.2 - - - +
343A LYS* 1.3 79.4 - - + +
345A THR* 1.3 61.5 + - - +
347A ALA* 3.8 3.6 + - - +
348A GLU* 3.6 19.8 + - - +
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Residues in contact with THR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASN* 4.4 7.0 - - + +
69A GLY* 4.0 22.9 - - - +
70A ILE* 4.0 14.3 - - + +
267A HIS* 4.2 14.4 + - + -
336A TYR* 4.3 3.4 + - - +
341A PHE 2.9 18.0 + - - -
342A TYR* 3.3 9.2 + - + -
344A GLU* 1.3 76.6 - - - +
346A LYS* 1.3 61.0 + - - +
348A GLU* 3.1 4.0 + - - +
349A LEU* 2.8 47.7 + - + +
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Residues in contact with LYS 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS* 3.1 26.5 + - - -
41A ASN* 3.9 9.7 + - - +
68A ASN* 3.4 33.8 - - + +
342A TYR* 3.0 50.5 + - + +
343A LYS* 4.5 4.5 - - - +
345A THR* 1.3 76.2 - - + +
347A ALA* 1.3 59.5 + - - +
349A LEU* 3.9 10.3 - - + -
350A HIS* 2.5 52.1 + - + -
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A LYS 3.2 20.0 + - - +
344A GLU* 4.2 5.2 - - - +
345A THR 3.2 0.6 - - - -
346A LYS* 1.3 77.6 - - - +
348A GLU* 1.3 58.2 + - - +
350A HIS* 4.4 4.1 - - - +
351A GLN* 3.8 18.2 + - - +
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Residues in contact with GLU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 3.7 24.9 - - + -
72A LYS* 5.1 15.1 + - - +
344A GLU 3.6 10.6 + - - +
345A THR 3.1 4.2 + - - +
347A ALA* 1.3 77.9 - - - +
349A LEU* 1.3 59.1 + - - +
350A HIS 3.3 1.3 - - - -
351A GLN* 2.9 31.7 + - - +
352A LEU* 2.9 47.3 + - + +
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A SER* 3.9 14.8 - - - +
39A PHE 3.9 7.2 - - - +
40A HIS* 3.9 36.1 + - + +
68A ASN* 3.7 29.8 - - + -
69A GLY 3.7 21.3 - - - +
70A ILE* 3.7 12.3 - - + -
345A THR* 2.8 30.4 + - + +
346A LYS* 4.1 12.1 - - + +
348A GLU* 1.3 77.6 - - - +
350A HIS* 1.3 57.4 + - - +
352A LEU* 3.6 3.9 + - - +
353A SER* 3.1 29.5 + - - -
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Residues in contact with HIS 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS* 4.0 21.4 + + - -
346A LYS* 2.5 58.9 + - + +
347A ALA* 4.8 4.0 - - - +
348A GLU 3.3 0.2 - - - -
349A LEU* 1.3 77.0 - - - +
351A GLN* 1.3 62.0 + - - +
353A SER* 4.0 16.7 + - - +
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Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A ALA 3.8 13.4 + - - +
348A GLU* 2.9 38.6 + - - +
350A HIS* 1.3 78.2 - - - +
352A LEU* 1.3 65.3 + - + +
353A SER 4.5 1.6 - - - -
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.5 20.2 - - + +
38A SER* 3.8 32.1 - - - +
70A ILE* 4.5 13.0 - - + -
72A LYS* 6.2 0.4 - - - +
107A LEU* 5.0 1.3 - - + -
109A ASN* 5.1 3.8 - - - -
110A GLY* 3.8 38.8 - - - +
348A GLU* 2.9 35.1 + - + +
349A LEU* 4.0 4.9 - - - +
351A GLN* 1.3 79.0 - - + +
353A SER* 1.3 61.5 + - - +
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A HIS* 5.0 11.9 + - - -
105A ASP* 5.0 7.8 + - - -
107A LEU* 4.4 19.2 - - - +
110A GLY 5.1 0.4 - - - -
349A LEU 3.1 19.6 + - - -
350A HIS* 4.0 15.7 - - - +
351A GLN 4.5 2.0 - - - -
352A LEU* 1.3 81.1 - - - +
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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