Contacts of the helix formed by residues 53 - 58 (chain H) in PDB entry 6AHU
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 GLY 53 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ARG 5.6 0.2 - - - -
40E VAL 3.3 10.1 - - - -
41E HIS 3.5 1.3 - - - -
42E GLY 3.5 8.1 - - - +
48H VAL 2.6 13.5 + - - +
49H LYS* 3.4 25.1 + - - -
52H PHE* 1.3 74.7 - - - +
54H GLU* 1.3 60.1 + - - -
55H VAL 3.3 3.1 + - - -
56H ASP 3.5 1.4 + - - -
57H ALA* 2.9 26.5 + - - +
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Residues in contact with GLU 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ARG 4.0 11.9 + - - +
40E VAL* 2.8 13.4 + - + +
49H LYS* 4.3 23.1 + - + +
53H GLY* 1.3 71.3 - - - -
55H VAL* 1.3 67.4 + - + +
57H ALA* 3.4 17.2 + - - +
58H ALA 3.8 3.5 + - - -
163I SER* 2.9 30.5 - - - +
166I ARG* 3.3 42.0 + - + +
167I ARG* 4.2 27.4 + - + +
170I ILE* 4.5 6.8 - - - +
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Residues in contact with VAL 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E VAL* 3.8 29.4 - - + +
41E HIS* 5.3 10.1 - - + +
83E PHE* 4.7 8.1 - - + -
52H PHE 5.5 0.4 - - - +
53H GLY 3.3 0.6 - - - -
54H GLU* 1.3 81.1 - - + +
56H ASP* 1.3 68.5 + - - +
58H ALA 3.7 9.2 + - - -
59H LEU* 4.4 3.6 + - - +
170I ILE* 3.8 40.8 - - + +
174I LEU* 5.6 0.2 - - - +
209I LEU* 3.8 35.4 - - + +
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Residues in contact with ASP 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E HIS* 5.2 5.3 + - - -
48H VAL* 3.3 16.9 - - + +
52H PHE* 3.4 41.8 + - + +
53H GLY 3.5 3.1 + - - +
55H VAL* 1.3 81.9 - - - +
57H ALA* 1.3 62.3 + - - +
58H ALA 3.3 1.3 - - - -
59H LEU* 3.3 36.8 + - + +
61H LEU* 5.5 1.9 - - - +
84H LYS* 3.2 38.2 + - + +
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Residues in contact with ALA 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LEU 5.4 0.2 - - - +
45H ILE* 3.7 53.0 - - + +
48H VAL* 4.2 9.7 - - - +
49H LYS* 4.4 4.3 - - + +
53H GLY 2.9 17.1 + - - +
54H GLU* 3.5 14.8 - - - +
55H VAL 3.2 1.2 - - - -
56H ASP* 1.3 79.5 - - - +
58H ALA* 1.3 56.6 + - + +
59H LEU 3.4 4.0 + - - +
61H LEU* 4.8 8.5 - - - +
167I ARG* 4.9 5.8 - - - +
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Residues in contact with ALA 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H ILE* 6.0 0.7 - - - -
54H GLU 3.8 1.0 + - - +
55H VAL 3.7 6.4 + - - -
56H ASP 3.3 0.6 - - - -
57H ALA* 1.3 77.1 - - - +
59H LEU* 1.3 64.3 + - - +
60H PRO* 3.8 1.2 - - - +
167I ARG* 3.5 40.6 - - + +
170I ILE* 3.7 16.2 - - + +
171I SER* 3.4 27.5 + - - -
174I LEU* 4.6 0.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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