Contacts of the helix formed by residues 33 - 40 (chain B) in PDB entry 3HA6
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 33 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A LYS* 4.8 0.9 - - - +
30B ASN 3.5 18.5 + - - -
31B ILE* 4.3 1.6 - - - -
32B ASP* 1.3 80.2 + - - +
34B TRP* 1.3 55.5 + - - +
35B PHE 3.1 2.7 - - - -
36B GLU* 2.9 16.4 + - - +
37B GLU* 2.8 52.9 + - - +
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Residues in contact with TRP 34 (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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183A GLU* 3.2 32.3 - - + -
184A ILE* 4.6 3.4 - - + -
187A HIS* 3.3 44.9 + + + -
280A HIS* 5.9 2.7 - - + -
11B ASP* 3.2 31.8 + - + -
31B ILE 3.4 18.4 + - - +
32B ASP 4.5 0.4 - - - -
33B SER* 1.3 78.3 + - - +
35B PHE* 1.3 88.8 + + - +
37B GLU* 3.7 13.7 + - + +
38B LYS* 2.9 76.6 + - + +
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Residues in contact with PHE 35 (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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184A ILE* 3.5 33.0 - - + -
187A HIS* 3.2 33.4 - - + -
188A LEU* 3.7 20.2 - - + -
250A LYS* 3.4 32.3 - - + +
252A VAL* 3.6 16.8 - - + -
280A HIS* 3.3 36.7 + + - +
32B ASP* 3.3 21.3 - - - +
33B SER 3.1 1.0 - - - -
34B TRP* 1.3 96.2 - + - +
36B GLU* 1.3 61.1 + - - +
38B LYS* 4.6 1.1 - - - -
39B ALA* 3.1 22.0 + - - +
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Residues in contact with GLU 36 (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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249A SER 3.8 13.3 - - - +
250A LYS* 3.3 33.1 + - - +
251A ARG* 5.9 0.7 - - - +
32B ASP 3.1 20.3 - - - +
33B SER* 2.9 14.5 + - - +
35B PHE* 1.3 77.6 - - - +
37B GLU* 1.3 60.1 + - + +
39B ALA* 3.6 5.5 + - - +
40B ASN* 3.1 41.4 + - - +
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Residues in contact with GLU 37 (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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33B SER* 2.8 30.5 + - - +
34B TRP* 3.7 21.9 + - + +
36B GLU* 1.3 77.2 - - + +
38B LYS* 1.3 63.2 + - - +
39B ALA 3.2 0.2 - - - -
40B ASN* 3.2 16.8 + - - +
41B LEU* 3.5 19.0 + - - +
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Residues in contact with LYS 38 (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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179A ARG* 6.1 0.2 - - - +
183A GLU* 3.4 18.2 + - - -
280A HIS* 4.8 12.6 - - + +
11B ASP* 4.1 11.5 + - - +
34B TRP* 2.9 62.8 + - + +
35B PHE* 4.1 4.7 - - - +
37B GLU* 1.3 76.3 - - - +
39B ALA* 1.3 60.6 - - - +
41B LEU* 3.4 32.3 - - + +
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Residues in contact with ALA 39 (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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251A ARG* 6.2 0.7 - - + -
280A HIS* 3.9 4.5 - - + +
282A PRO* 3.8 31.9 - - + -
35B PHE 3.1 19.5 + - - +
36B GLU* 3.8 7.4 - - - +
37B GLU 3.2 0.2 - - - -
38B LYS* 1.3 75.2 - - - +
40B ASN* 1.3 59.2 + - - +
41B LEU 3.1 15.9 + - - +
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Residues in contact with ASN 40 (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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36B GLU* 3.1 27.6 + - - +
37B GLU* 3.2 10.3 + - - +
39B ALA* 1.3 76.5 - - - +
41B LEU* 1.3 61.2 + - - +
42B GLU* 3.5 4.5 + - - +
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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