Contacts of the helix formed by residues 130 - 146 (chain C) in PDB entry 4DDG
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 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C ILE* 2.7 23.4 + - + +
127C TYR 4.5 0.2 - - - -
129C THR* 1.3 81.2 + - - +
131C ARG* 1.3 64.3 + - - +
132C GLU* 3.3 19.6 + - - +
133C LYS* 3.1 38.6 + - + +
134C TYR 3.5 12.0 + - - -
136C ARG* 5.2 0.7 + - - -
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Residues in contact with ARG 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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127C TYR* 3.3 72.6 + - - +
129C THR 3.9 3.8 + - - +
130C ASP* 1.3 72.2 + - - +
132C GLU* 1.3 66.5 + - - +
134C TYR* 3.2 4.5 + - - +
135C ASN* 2.9 46.5 + - - +
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Residues in contact with GLU 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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130C ASP* 3.3 14.8 + - - +
131C ARG* 1.3 79.3 - - - +
133C LYS* 1.3 64.9 + - - +
135C ASN* 3.2 5.8 + - - +
136C ARG* 2.9 39.5 + - - +
139C ARG* 5.3 5.4 + - - -
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Residues in contact with LYS 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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126C ILE* 3.7 33.0 - - + -
130C ASP* 3.1 29.8 + - - +
131C ARG 3.4 0.4 - - - -
132C GLU* 1.3 80.1 - - - +
134C TYR* 1.3 58.5 + - - +
136C ARG* 3.4 29.2 - - - +
137C ILE* 2.9 59.4 + - + +
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Residues in contact with TYR 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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44C PRO* 4.5 11.4 - - + -
45C TYR* 2.4 31.6 + + - -
74C TYR* 3.6 28.6 - + - -
75C HIS* 4.0 3.5 - - - -
76C PRO* 3.9 13.8 - - + +
113C PRO* 4.5 5.9 - - + +
123C ILE* 3.9 20.9 - - + -
126C ILE* 3.9 8.0 - - + +
127C TYR* 3.4 53.5 - + + -
130C ASP 3.5 11.8 + - - +
131C ARG* 3.2 9.3 + - - +
132C GLU 3.2 0.4 - - - -
133C LYS* 1.3 78.4 - - - +
135C ASN* 1.3 80.6 + - - +
137C ILE* 3.9 0.9 - - - +
138C ALA* 2.9 34.7 + - + +
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Residues in contact with ASN 135 (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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44C PRO* 3.5 24.9 - - + +
131C ARG* 2.9 32.9 + - - +
132C GLU* 3.7 4.6 - - - +
134C TYR* 1.3 93.4 - - - +
136C ARG* 1.3 58.4 + - - +
139C ARG* 2.9 57.0 + - - +
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Residues in contact with ARG 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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130C ASP* 5.2 0.6 + - - -
132C GLU* 2.9 28.7 + - - +
133C LYS* 3.4 40.1 - - - +
135C ASN* 1.3 76.2 - - - +
137C ILE* 1.3 70.8 + - - +
139C ARG* 3.2 16.3 + - - +
140C GLU* 2.9 46.4 + - - +
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Residues in contact with ILE 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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74C TYR* 3.5 48.5 - - + +
126C ILE* 5.1 0.7 - - + -
133C LYS* 2.9 50.9 + - + +
134C TYR 3.9 2.5 - - - +
136C ARG* 1.3 81.4 - - - +
138C ALA* 1.3 58.2 + - - +
140C GLU* 3.0 16.4 + - - +
141C TRP* 2.9 39.2 + - + +
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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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44C PRO* 3.7 23.6 - - + -
45C TYR* 4.4 10.7 - - + +
74C TYR* 3.9 31.8 + - + +
134C TYR* 2.9 22.0 + - + +
137C ILE* 1.3 77.2 - - - +
139C ARG* 1.3 53.5 + - - +
141C TRP* 3.4 2.4 + - - +
142C THR* 2.7 38.3 + - - -
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Residues in contact with ARG 139 (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 SER 4.6 3.8 + - - -
44C PRO* 3.3 38.2 - - + +
132C GLU* 5.1 5.1 + - - -
135C ASN* 2.9 49.2 + - - +
136C ARG* 3.5 12.2 - - - +
138C ALA* 1.3 78.0 - - - +
140C GLU* 1.3 56.8 + - + +
142C THR* 3.3 2.9 + - - -
143C GLN* 2.9 34.8 + - + +
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Residues in contact with GLU 140 (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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136C ARG* 2.9 43.5 + - - +
137C ILE* 3.0 18.2 + - - +
139C ARG* 1.3 78.4 - - + +
141C TRP* 1.3 62.4 + - + +
143C GLN* 3.2 10.7 + - + +
144C LYS* 2.9 42.5 + - - +
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Residues in contact with TRP 141 (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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72C ARG* 3.5 31.2 - - + +
73C ILE* 3.4 25.4 - - - -
74C TYR* 3.3 53.8 - + + +
80C SER* 4.8 11.4 - - - -
123C ILE* 5.6 2.7 - - + -
137C ILE* 2.9 32.2 + - + +
138C ALA 3.7 4.5 - - - +
140C GLU* 1.3 77.8 - - + +
142C THR* 1.3 61.5 + - - +
144C LYS* 4.6 5.2 - - + -
145C TYR* 2.9 57.8 + + + +
146C ALA 3.9 0.2 + - - -
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Residues in contact with THR 142 (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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44C PRO 3.7 3.9 + - - -
45C TYR* 3.6 37.8 - - - +
46C GLN 4.2 5.2 - - - +
48C GLY* 3.6 31.4 - - - +
50C PHE* 4.2 5.8 - - + -
138C ALA 2.7 22.0 + - - -
139C ARG* 3.5 6.1 - - - -
140C GLU 3.2 0.2 - - - -
141C TRP* 1.3 76.3 - - - +
143C GLN* 1.3 62.7 + - - +
146C ALA* 3.0 28.9 + - + -
147C MET* 3.1 16.1 + - + +
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Residues in contact with GLN 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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139C ARG* 2.9 19.0 + - + +
140C GLU* 3.3 13.7 - - + +
142C THR* 1.3 77.0 - - - +
144C LYS* 1.3 61.8 + - + +
147C MET* 3.5 43.8 - - + +
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Residues in contact with LYS 144 (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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140C GLU* 2.9 28.9 + - - +
141C TRP* 3.9 7.6 - - + +
142C THR 3.1 0.2 - - - -
143C GLN* 1.3 81.9 - - + +
145C TYR* 1.3 96.1 + - + +
146C ALA 3.6 0.4 + - - -
147C MET 4.2 2.8 + - - -
148C GLY* 4.5 6.6 + - - -
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Residues in contact with TYR 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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81A ASN* 5.6 3.8 + - - -
71C THR* 3.9 7.8 - - - +
72C ARG* 3.6 68.5 + - + +
141C TRP* 2.9 63.8 + + + +
144C LYS* 1.3 99.8 + - + +
146C ALA* 1.3 58.9 + - - +
147C MET 3.4 0.6 + - - -
148C GLY* 4.3 5.7 + - - -
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Residues in contact with ALA 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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48C GLY* 3.9 4.7 - - - -
49C VAL* 3.2 44.5 + - - +
50C PHE* 3.7 31.4 - - + -
71C THR* 3.9 3.6 - - + -
141C TRP 3.9 1.0 + - - +
142C THR* 3.0 14.8 + - + +
145C TYR* 1.3 78.4 - - + +
147C MET* 1.3 61.8 + - - +
148C GLY 3.5 0.9 - - - -
1025C ALA* 3.7 12.0 - - - +
1026C TYR* 6.0 0.3 - - - -
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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