Contacts of the helix formed by residues 120 - 129 (chain C) in PDB entry 4DDI
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 VAL 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C PRO 3.0 12.2 + - - +
78C ILE 4.3 4.7 - - - +
79C ASN* 3.7 30.1 - - + -
80C SER* 4.4 7.9 - - - +
118C PRO* 3.7 4.3 - - - +
119C LEU* 1.3 81.0 - - - +
121C PRO* 1.3 69.8 - - + +
122C GLU* 3.2 13.9 + - + +
123C ILE* 3.4 31.5 + - + +
124C ALA 3.3 14.9 + - - -
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Residues in contact with PRO 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C PRO* 4.0 17.0 - - + +
119C LEU 3.9 7.2 - - - +
120C VAL* 1.3 87.2 - - + +
122C GLU* 1.3 61.5 + - + +
124C ALA* 3.5 2.7 + - + +
125C ARG* 2.9 28.1 + - - +
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Residues in contact with GLU 122 (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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74C TYR* 5.5 2.2 - - - +
120C VAL* 3.2 9.9 - - + -
121C PRO* 1.3 81.7 - - + +
123C ILE* 1.3 62.3 + - + +
125C ARG* 3.1 38.5 + - - +
126C ILE* 2.9 46.2 + - + +
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Residues in contact with ILE 123 (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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73C ILE 5.2 1.1 - - - +
74C TYR* 3.5 58.6 - - + -
75C HIS 3.1 24.7 - - - +
76C PRO* 3.5 28.7 - - + -
78C ILE 4.7 2.5 - - - +
80C SER* 6.1 1.3 - - - +
120C VAL* 3.4 27.1 + - + +
122C GLU* 1.3 73.7 - - + +
124C ALA* 1.3 59.7 + - - +
126C ILE* 3.4 2.0 + - - +
127C TYR* 2.9 27.4 + - - +
134C TYR* 3.8 6.3 - - + -
141C TRP* 5.5 2.9 - - + -
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Residues in contact with ALA 124 (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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76C PRO* 3.7 14.5 - - + +
115C PRO* 3.5 28.2 - - + +
118C PRO* 3.5 26.9 - - + -
120C VAL 3.3 3.4 + - - +
121C PRO 3.5 6.5 - - - +
123C ILE* 1.3 80.4 - - - +
125C ARG* 1.3 56.4 + - - +
127C TYR* 3.2 5.8 + - - +
128C LYS* 2.9 31.8 + - - +
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Residues in contact with ARG 125 (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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121C PRO 2.9 18.3 + - - +
122C GLU* 3.1 30.0 + - - +
124C ALA* 1.3 76.7 - - - +
126C ILE* 1.3 82.5 + - - +
128C LYS* 3.4 5.0 + - - +
129C THR* 2.9 47.4 + - + +
133C LYS* 5.8 1.0 - - - +
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Residues in contact with ILE 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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74C TYR* 3.9 18.8 - - - +
122C GLU* 2.9 32.2 + - + +
123C ILE 3.8 4.3 - - - +
125C ARG* 1.3 100.6 - - - +
127C TYR* 1.3 65.5 + - - +
129C THR* 3.8 4.3 - - - +
130C ASP* 2.8 46.1 + - + +
133C LYS* 3.6 32.1 - - + -
134C TYR* 3.7 23.8 - - + +
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Residues in contact with TYR 127 (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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76C PRO* 4.9 2.9 - - + -
112C ASP* 5.1 3.6 + - - -
113C PRO* 3.6 39.3 + - + +
115C PRO* 3.7 37.2 - - + -
123C ILE 2.9 17.7 + - - +
124C ALA* 3.2 7.8 + - - +
126C ILE* 1.3 79.1 - - - +
128C LYS* 1.3 62.7 + - + +
129C THR* 3.3 2.6 + - - -
131C ARG* 2.9 68.1 + - - +
134C TYR* 3.8 34.0 - + + -
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Residues in contact with LYS 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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115C PRO* 4.1 33.7 + - + +
116C ASP* 4.2 23.8 - - - +
124C ALA 2.9 14.5 + - - +
125C ARG* 4.1 4.9 - - - +
127C TYR* 1.3 79.3 - - + +
129C THR* 1.3 64.5 - - + +
131C ARG* 4.9 1.3 - - - +
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Residues in contact with THR 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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125C ARG* 2.9 42.0 + - + +
126C ILE* 3.7 5.4 + - - +
127C TYR 3.2 1.5 - - - +
128C LYS* 1.3 85.9 - - + +
130C ASP* 1.3 72.1 + - - +
131C ARG* 3.7 3.3 + - - +
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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