Contacts of the helix formed by residues 119 - 128 (chain C) in PDB entry 3DLX
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 ASN 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C ALA* 2.7 30.0 + - + +
93C GLY 4.3 2.2 - - - +
94C VAL 3.3 16.4 + - - -
95C ASP* 3.5 13.2 - - - +
100C GLY* 3.6 10.1 - - - -
103C LEU* 4.3 3.3 - - - +
116C VAL 4.5 4.6 + - - +
117C GLY 3.3 6.8 - - - +
118C GLU* 1.3 79.1 - - - +
120C ALA* 1.3 64.4 + - - +
121C GLU* 3.1 12.8 + - - +
122C PHE* 3.0 33.2 + - + +
123C GLU* 3.2 19.6 + - - +
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Residues in contact with ALA 120 (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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95C ASP* 2.7 18.0 + - - +
118C GLU 4.2 0.2 - - - -
119C ASN* 1.3 72.8 - - - +
121C GLU* 1.3 55.4 + - - +
123C GLU* 3.5 13.1 + - - +
124C ARG* 3.1 28.1 + - - +
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Residues in contact with GLU 121 (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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95C ASP* 3.3 18.3 + - - +
100C GLY 5.7 0.7 - - - +
103C LEU* 4.3 4.4 - - + +
104C ARG* 3.8 40.0 + - + +
106C LYS* 6.0 0.3 - - - +
119C ASN* 3.1 5.8 + - - +
120C ALA* 1.3 76.6 - - - +
122C PHE* 1.3 65.4 + - - +
124C ARG* 3.1 35.4 + - - +
125C GLN* 3.1 46.7 + - - +
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Residues in contact with PHE 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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92C ALA* 3.9 9.0 - - + -
103C LEU* 3.8 22.9 - - + +
111C MET* 4.3 8.3 - - + -
116C VAL* 3.2 53.8 - - + -
119C ASN* 3.0 29.8 + - + +
121C GLU* 1.3 74.7 - - - +
123C GLU* 1.3 64.6 + - + +
125C GLN* 3.2 5.6 + - - +
126C TYR* 2.8 50.9 + + + +
131C LEU* 3.4 26.7 - - + -
133C VAL* 3.4 27.1 - - + -
420C VAL 5.2 0.4 - - - -
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Residues in contact with GLU 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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119C ASN 3.2 9.3 + - - +
120C ALA* 3.6 14.2 - - - +
122C PHE* 1.3 88.1 - - + +
124C ARG* 1.3 60.1 + - - +
126C TYR* 4.5 2.0 - - - -
127C LEU* 2.9 57.5 + - + +
421C LYS* 6.0 1.7 - - - +
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Residues in contact with ARG 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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120C ALA 3.1 16.9 + - - +
121C GLU* 3.1 38.1 + - - +
122C PHE 3.2 0.2 - - - -
123C GLU* 1.3 80.7 - - + +
125C GLN* 1.3 64.0 + - - +
127C LEU* 4.8 1.7 - - - +
128C SER* 2.6 40.2 + - - -
130C GLU* 2.9 33.8 + - - -
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Residues in contact with GLN 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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103C LEU* 2.5 48.5 + - - +
106C LYS* 4.9 10.1 - - - +
108C ILE 4.7 4.9 - - - +
121C GLU* 3.1 36.3 + - - +
122C PHE* 3.2 3.8 + - - +
124C ARG* 1.3 92.6 - - - +
126C TYR* 1.3 63.3 + - - +
128C SER* 3.4 4.4 + - - -
129C GLY 3.3 1.7 + - - -
130C GLU* 2.7 47.9 + - + +
131C LEU* 3.1 26.7 + - + +
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Residues in contact with TYR 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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116C VAL* 5.1 0.7 - - + -
122C PHE* 2.8 46.8 + + + +
123C GLU* 3.8 3.4 - - - +
125C GLN* 1.3 78.8 - - - +
127C LEU* 1.3 67.8 + - + +
129C GLY* 3.4 10.9 + - - -
131C LEU* 3.9 15.0 - - + +
133C VAL* 3.5 28.5 - - + -
135C LEU* 3.5 18.1 - - + +
171C PRO* 2.9 24.5 + - - +
172C ILE 3.9 14.1 - - - -
174C TYR* 3.6 34.3 + + - +
420C VAL* 3.7 35.5 - - + +
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Residues in contact with LEU 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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123C GLU* 2.9 45.5 + - + +
124C ARG* 4.8 2.0 - - - +
126C TYR* 1.3 81.3 - - + +
128C SER* 1.3 59.0 + - - +
129C GLY 3.4 0.2 - - - -
174C TYR* 3.7 43.5 - - + +
175C ASN 3.7 9.4 - - - +
176C LYS* 4.4 4.3 - - - +
178C GLY* 5.7 0.7 - - - -
417C GLY 5.2 10.5 - - - +
418C LYS 5.0 11.4 - - - +
420C VAL* 5.0 11.2 - - + -
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Residues in contact with SER 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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124C ARG* 2.6 27.7 + - - -
125C GLN 3.4 5.7 + - - -
127C LEU* 1.3 77.7 - - - +
129C GLY* 1.3 59.0 + - - +
130C GLU* 3.3 23.5 + - - +
174C TYR 4.3 2.2 - - - -
175C ASN* 5.4 0.2 - - - -
176C LYS* 3.8 44.1 + - - +
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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