Contacts of the helix formed by residues 142 - 146 (chain C) in PDB entry 2HU4
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 142 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ARG 3.6 3.5 - - - +
108A ILE 5.2 0.2 - - - +
110A SER* 2.6 34.3 + - - +
111A LYS* 3.9 21.2 - - + +
139C LEU* 3.5 20.7 + - + +
140C LEU 3.2 0.8 - - - +
141C ASN* 1.3 80.1 - - - +
143C LYS* 1.3 64.2 + - - +
144C HIS* 2.9 35.0 + - - +
145C SER* 2.9 24.8 - - - +
146C ASN 4.4 0.2 + - - -
437C ILE* 5.2 0.7 - - - +
468C ILE 4.1 8.0 - - - +
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Residues in contact with LYS 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A SER* 4.1 15.3 - - - +
463A GLU* 3.1 51.1 + - - +
465A PRO 3.0 27.9 + - - -
466A PHE* 4.1 10.2 - - - +
467A THR 5.1 1.0 - - - +
142C ASP* 1.3 70.5 + - - +
144C HIS* 1.3 72.0 + - + +
145C SER 2.7 10.5 + - - -
146C ASN* 2.9 23.6 + - - +
437C ILE* 4.9 5.9 - - - +
468C ILE 5.3 3.1 - - - -
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Residues in contact with HIS 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 3.1 48.0 + - + +
110A SER* 3.1 18.5 + - - -
461A GLY 4.1 4.4 + - - -
462A ALA* 3.6 11.7 - - + -
463A GLU* 3.1 47.0 + - + +
466A PHE* 3.8 12.7 - - - -
138C ALA* 3.3 25.0 - - + +
142C ASP* 2.9 26.2 + - - +
143C LYS* 1.3 78.8 - - + +
145C SER* 1.3 57.5 + - - +
146C ASN* 3.1 4.1 + - - +
148C THR* 4.2 4.9 - - - +
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Residues in contact with SER 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C VAL* 5.2 4.9 - - - +
138C ALA* 4.1 4.2 - - - +
139C LEU 3.4 19.9 + - - -
140C LEU* 4.9 2.7 - - - +
141C ASN 4.7 4.3 + - - -
142C ASP 2.9 19.2 + - - -
143C LYS 2.7 0.8 + - - -
144C HIS* 1.3 79.4 - - - +
146C ASN* 1.3 71.0 - - - +
148C THR* 2.9 23.0 + - - -
437C ILE* 4.8 1.2 - - - +
438C TRP* 3.0 29.2 - - - +
468C ILE 5.3 0.8 + - - -
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Residues in contact with ASN 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A GLU* 5.2 6.6 - - - +
143C LYS 2.9 14.3 + - - +
144C HIS* 3.1 3.2 - - - -
145C SER* 1.3 89.7 - - - +
147C GLY* 1.3 56.0 + - - +
148C THR* 2.4 16.8 + - - -
430C ARG* 5.3 0.8 - - - +
437C ILE* 2.4 58.8 + - - +
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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