Contacts of the helix formed by residues 125 - 130 (chain C) in PDB entry 4JUO
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 125 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C VAL* 6.6 0.2 - - - -
100C THR* 2.7 39.7 + - - +
101C ILE* 5.0 0.9 - - - +
102C LEU 5.0 1.8 - - - +
122C VAL* 4.1 17.0 + - - -
123C GLY 3.7 0.8 - - - -
124C SER* 1.3 73.8 - - - +
126C VAL* 1.3 63.6 + - - +
127C VAL* 3.0 21.4 - - - +
128C ASN* 2.9 26.5 + - - +
129C ALA* 3.1 11.6 + - - +
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Residues in contact with VAL 126 (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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25C VAL* 4.3 17.5 - - + -
32C TYR* 4.3 21.1 - - + +
33C ILE* 3.8 27.4 - - + -
44C LEU* 4.8 3.1 - - + -
47C GLU* 5.5 1.8 - - + -
102C LEU* 3.2 43.6 - - + +
103C HIS* 4.0 12.1 - - + +
124C SER* 3.6 8.2 - - - +
125C SER* 1.3 70.5 - - - +
127C VAL* 1.3 60.0 + - - +
129C ALA* 4.1 6.3 - - - -
130C LEU* 3.2 29.6 - - + +
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 3.8 29.4 - - + +
48C ILE* 3.5 38.4 - - + -
100C THR* 4.2 2.7 - - + -
102C LEU* 3.1 20.6 - - + +
125C SER* 3.2 16.4 - - - +
126C VAL* 1.3 76.2 - - - +
128C ASN* 1.3 64.4 + - - +
129C ALA 3.0 1.8 - - - -
130C LEU 2.6 23.6 + - - -
131C SER* 3.0 16.5 + - - -
134C LEU* 4.2 17.3 - - + -
176C PHE* 4.4 13.4 - - + -
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Residues in contact with ASN 128 (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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100C THR* 5.6 1.1 - - + -
122C VAL* 3.4 33.3 + - + +
125C SER* 2.9 23.2 + - - +
127C VAL* 1.3 81.1 - - + +
129C ALA* 1.3 57.1 + - - +
131C SER* 3.1 14.3 + - - -
134C LEU* 4.3 13.7 - - + +
149C PHE* 3.6 22.0 - - - +
151C ASN 3.1 19.1 - - - +
152C GLY 3.6 4.6 + - - +
153C GLY* 3.3 35.1 + - - -
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Residues in contact with ALA 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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24C ALA 5.4 2.9 - - - +
25C VAL* 3.7 25.8 - - + -
26C ARG* 3.1 41.4 + - + +
124C SER* 5.8 0.9 - - - -
125C SER 3.1 11.6 + - - +
126C VAL 4.0 0.9 - - - +
127C VAL 3.0 0.2 - - - -
128C ASN* 1.3 80.1 - - - +
130C LEU* 1.3 71.2 + - + +
151C ASN 3.4 2.3 - - - +
152C GLY* 3.7 13.2 + - - +
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Residues in contact with LEU 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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25C VAL* 3.6 26.0 - - + +
26C ARG* 4.3 18.4 - - - +
29C PRO* 4.7 7.2 - - + +
32C TYR* 6.0 0.2 - - + -
33C ILE* 3.5 33.4 - - + -
44C LEU* 4.0 7.1 - - + +
126C VAL* 3.2 17.3 - - + +
127C VAL* 2.6 13.8 + - - +
129C ALA* 1.3 80.4 - - + +
131C SER* 1.3 54.9 + - - -
176C PHE* 5.2 0.5 - - - -
178C PRO* 3.4 16.6 - - - +
179C ASP* 3.5 6.3 + - - -
182C ILE* 3.7 23.6 - - + -
183C PHE* 3.8 28.2 - - + -
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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