Contacts of the helix formed by residues 55 - 59 (chain F) in PDB entry 4HHM
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 ASP 55 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53F PHE* 4.4 4.3 - - - -
54F HIS* 1.3 70.5 - - - +
56F ASP* 1.3 78.4 + - - +
57F ASP 3.2 0.2 + - - -
58F LEU* 3.3 2.3 + - - -
59F ILE* 2.9 35.2 + - + +
68F ARG* 5.6 7.2 - - - +
90F THR 3.1 7.1 + - - -
91F THR* 3.4 18.1 - - - +
92F ASN 2.9 17.3 + - - -
118F LYS* 2.6 29.7 + - - +
122F ASN* 3.1 34.9 - - + +
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Residues in contact with ASP 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F HIS 3.1 1.2 + - - -
55F ASP* 1.3 92.3 + - - +
57F ASP* 1.3 63.6 + - - +
58F LEU 3.4 0.2 - - - -
59F ILE 3.4 19.7 - - - +
60F PRO* 4.2 6.1 - - - +
61F PHE* 4.7 20.1 - - + +
92F ASN* 3.5 37.8 + - + +
95F THR* 5.1 4.2 - - - +
96F HIS* 5.7 2.8 + - - +
118F LYS* 2.7 30.9 + - - -
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Residues in contact with ASP 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 4.3 20.4 - - + -
16F TRP* 3.5 27.3 + - - +
36F PRO* 3.6 21.1 - - - +
53F PHE* 4.3 0.3 - - - -
54F HIS* 2.9 47.7 + - - +
56F ASP* 1.3 82.4 - - - +
58F LEU* 1.3 60.7 + - - +
92F ASN* 5.3 3.5 + - - -
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Residues in contact with LEU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LEU* 5.0 2.2 - - + -
36F PRO* 4.6 11.3 - - + +
53F PHE* 3.7 36.6 - - + -
54F HIS 3.6 0.8 + - - -
55F ASP 3.3 1.9 + - - +
57F ASP* 1.3 82.3 - - - +
59F ILE* 1.3 76.7 + - + +
60F PRO* 4.0 2.5 - - - +
71F HIS* 3.5 29.2 + - - +
72F VAL* 4.3 15.5 - - + -
75F PHE* 3.4 55.6 - - + -
125F LEU* 4.3 4.3 - - + -
129F LEU* 4.3 4.9 - - + -
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Residues in contact with ILE 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ASP* 2.9 19.9 + - + +
56F ASP* 3.4 14.0 - - - +
58F LEU* 1.3 109.4 - - + +
60F PRO* 1.3 68.5 - - + +
61F PHE* 3.5 0.7 + - - -
63F ALA* 3.5 29.2 - - + +
68F ARG* 3.9 46.4 - - + +
71F HIS* 4.6 1.8 - - + -
72F VAL* 3.7 20.6 - - + -
122F ASN* 5.5 0.2 - - - +
125F LEU* 3.9 12.6 - - + -
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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