Contacts of the helix formed by residues 128 - 138 (chain C) in PDB entry 5HJD
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 THR 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ARG* 4.1 2.8 + - - -
93C GLU* 3.1 39.2 + - + +
127C PRO* 1.3 79.6 - - - +
129C GLU* 1.3 60.5 + - - +
130C ASP* 2.4 43.5 + - - +
131C PHE* 3.9 4.7 - - - +
132C ARG* 3.3 14.2 - - - +
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Residues in contact with GLU 129 (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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129A GLU* 3.7 10.2 - - + +
132A ARG* 3.7 22.8 - - - +
133A ARG* 2.2 51.8 + - + +
128C THR* 1.3 71.0 - - - +
130C ASP* 1.3 71.3 + - - +
132C ARG* 3.8 3.2 - - - +
133C ARG* 2.3 62.4 + - - +
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Residues in contact with ASP 130 (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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93C GLU* 5.9 0.2 - - - +
128C THR* 2.4 33.6 + - - +
129C GLU* 1.3 77.7 - - - +
131C PHE* 1.3 57.8 + - + +
132C ARG 2.7 15.2 + - - -
133C ARG* 3.5 20.5 + - - +
134C LYS* 5.2 5.2 - - - +
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Residues in contact with PHE 131 (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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47C PHE* 3.9 19.5 - - + -
89C PHE* 3.9 15.3 - - + -
90C LYS* 3.9 18.2 - - + +
91C ASN* 3.6 40.6 - - + -
93C GLU* 4.4 6.5 - - - +
124C PHE* 3.9 27.4 - + - -
127C PRO* 4.2 15.5 - - + -
128C THR* 3.9 6.3 - - - +
129C GLU 3.9 0.2 + - - -
130C ASP* 1.3 74.6 - - + +
132C ARG* 1.3 61.7 + - - +
133C ARG 3.2 1.5 - - - +
134C LYS* 3.0 36.9 + - + +
135C LEU* 3.0 45.7 + - + +
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Residues in contact with ARG 132 (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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5A CYS* 3.9 16.7 - - - +
126A ASN 5.5 0.4 - - - -
127A PRO* 3.5 24.5 + - - +
129A GLU* 4.4 16.9 + - - +
132A ARG* 3.0 57.0 - - - +
7C VAL* 3.9 25.1 - - + -
127C PRO* 4.0 7.4 - - + -
128C THR 3.3 17.7 + - - +
129C GLU* 3.8 4.3 - - - +
130C ASP 2.7 8.7 + - - -
131C PHE* 1.3 74.5 - - - +
133C ARG* 1.3 64.7 + - - +
134C LYS 3.2 0.5 + - - -
135C LEU* 3.2 10.7 + - - +
136C LEU* 3.2 54.5 + - + +
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Residues in contact with ARG 133 (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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129A GLU* 2.5 35.1 + - - +
129C GLU* 2.3 43.2 + - - +
130C ASP* 3.5 24.4 + - - +
131C PHE 3.2 0.6 - - - +
132C ARG* 1.3 80.3 - - - +
134C LYS* 1.3 67.5 + - + +
136C LEU* 4.4 4.0 - - - +
137C LYS* 3.5 25.8 + - - +
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Residues in contact with LYS 134 (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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46C HIS* 3.3 42.1 + - + +
47C PHE* 4.4 5.2 - - - -
90C LYS* 4.0 32.9 + - - +
130C ASP* 5.2 4.7 - - - +
131C PHE* 3.0 31.9 + - + +
133C ARG* 1.3 82.3 - - + +
135C LEU* 1.3 59.0 + - - +
136C LEU 3.2 0.2 - - - -
137C LYS* 3.1 4.7 + - - +
138C ALA* 3.0 29.2 + - - +
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A SER* 3.2 19.5 + - - -
7C VAL* 3.9 24.0 - - + -
9C VAL* 3.6 25.3 - - + +
47C PHE* 4.0 17.9 - - + -
124C PHE* 3.7 30.1 - - + -
127C PRO* 4.8 4.3 - - + -
131C PHE* 3.0 53.3 + - + +
132C ARG* 3.2 15.9 + - + +
134C LYS* 1.3 76.0 - - - +
136C LEU* 1.3 59.3 + - - +
138C ALA* 3.3 17.0 + - - +
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Residues in contact with LEU 136 (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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1A MET* 4.7 12.7 - - - +
3A SER* 3.4 19.9 + - - +
4A SER* 3.9 31.2 - - - +
5A CYS* 4.2 11.7 - - + +
126A ASN* 4.3 9.0 - - + +
7C VAL* 4.5 8.5 - - + -
132C ARG* 3.2 56.2 + - + +
133C ARG* 4.8 3.1 - - - +
135C LEU* 1.3 73.7 - - - +
137C LYS* 1.3 64.0 + - - +
138C ALA 3.1 3.6 - - - +
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Residues in contact with LYS 137 (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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43C ASN* 5.7 1.4 - - - +
46C HIS* 3.3 40.6 - - + +
133C ARG* 3.5 22.6 + - - +
134C LYS* 3.1 7.3 + - - +
136C LEU* 1.3 77.5 - - - +
138C ALA* 1.3 61.0 + - - +
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Residues in contact with ALA 138 (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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1A MET* 3.8 13.9 - - - +
2A ALA 4.1 5.1 + - - +
3A SER* 2.9 27.5 + - - -
9C VAL* 5.2 1.6 - - + -
42C SER* 3.2 31.4 - - - -
43C ASN 3.5 26.3 + - - +
44C ILE* 4.5 1.0 - - + +
46C HIS* 4.1 3.8 - - + -
47C PHE* 3.6 28.9 - - + -
134C LYS 3.0 12.5 + - - +
135C LEU 3.4 12.3 - - - +
136C LEU 3.1 2.3 - - - +
137C LYS* 1.3 81.6 - - - +
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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