Contacts of the helix formed by residues 126 - 138 (chain C) in PDB entry 6W4E
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 126 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C ILE* 6.2 0.2 - - - -
123C ARG* 4.8 10.4 + - - +
124C THR 3.6 3.4 + - - +
125C VAL* 1.3 76.1 - - - +
127C THR* 1.3 80.1 + - - +
128C LYS* 2.8 49.6 + - + +
129C GLN* 2.9 34.1 + - + +
130C ALA* 3.1 8.1 + - - +
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Residues in contact with THR 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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154B ASP* 4.7 5.6 - - + +
123C ARG* 3.1 17.3 + - - +
125C VAL 4.1 0.8 + - - -
126C ASP* 1.3 78.5 + - - +
128C LYS* 1.3 58.0 + - - +
130C ALA* 3.5 5.7 - - - +
131C GLN* 2.8 61.9 + - - +
141C PHE* 3.8 9.0 - - + -
143C GLU* 2.7 40.8 + - - +
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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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45B VAL* 3.3 29.4 - - - +
46B ILE* 5.0 2.2 - - + +
47B ASP* 3.7 34.1 - - - +
48B GLY* 3.8 9.4 - - - +
157B TYR* 6.2 7.2 - - + -
161B ARG* 4.2 5.6 - - - +
126C ASP* 2.8 42.6 + - + +
127C THR* 1.3 78.1 - - - +
129C GLN* 1.3 59.7 + - - +
131C GLN* 3.5 9.9 + - - +
132C ASP* 3.0 26.2 + - - +
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Residues in contact with GLN 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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87C THR* 6.1 2.4 - - - +
90C PHE* 3.4 27.9 - - + -
124C THR 3.6 5.9 - - - +
125C VAL* 3.2 20.7 - - + +
126C ASP* 2.9 38.3 + - + +
128C LYS* 1.3 76.5 - - - +
130C ALA* 1.3 64.7 + - - +
132C ASP* 3.3 10.2 - - + +
133C LEU* 3.0 19.8 + - - +
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Residues in contact with ALA 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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82C PHE* 4.2 13.0 - - + -
84C ILE* 5.9 0.7 - - + -
90C PHE* 3.8 11.0 - - - -
113C LEU* 3.5 14.7 - - - +
125C VAL* 4.3 4.9 - - + -
126C ASP 3.1 14.4 + - - +
127C THR* 3.1 9.6 + - - +
129C GLN* 1.3 79.9 - - - +
131C GLN* 1.3 60.6 + - - +
133C LEU* 3.5 1.0 + - - +
134C ALA* 3.3 16.8 + - - +
141C PHE* 3.5 32.5 - - + -
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Residues in contact with GLN 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASP* 2.9 31.5 + - - -
161B ARG* 2.7 40.7 + - + +
127C THR* 2.8 39.9 + - - +
128C LYS* 3.8 3.9 + - - +
130C ALA* 1.3 74.1 - - - +
132C ASP* 1.3 59.4 + - - +
133C LEU 3.4 0.2 - - - -
134C ALA* 3.4 7.2 + - - +
135C ARG* 2.9 30.4 + - - +
141C PHE* 3.6 22.3 + - + +
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Residues in contact with ASP 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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47B ASP* 5.5 5.4 - - + +
128C LYS 3.0 15.3 + - - +
129C GLN* 3.3 15.0 - - - +
131C GLN* 1.3 76.9 - - - +
133C LEU* 1.3 64.9 + - - +
135C ARG* 2.7 51.2 + - - +
136C SER* 3.3 13.0 + - - -
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Residues in contact with LEU 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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90C PHE* 3.9 31.0 - - + +
93C ILE* 3.8 33.4 - - + -
94C HIS* 5.0 8.1 - - + +
113C LEU* 4.8 5.4 - - + -
129C GLN 3.0 15.4 + - - +
130C ALA 3.9 4.5 - - - +
132C ASP* 1.3 79.5 + - - +
134C ALA* 1.3 64.4 + - - +
136C SER* 3.3 7.7 + - - +
137C TYR* 3.2 52.1 + - + +
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Residues in contact with ALA 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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113C LEU* 4.3 7.5 - - + +
130C ALA 3.3 12.0 + - - +
131C GLN* 3.6 8.7 - - - +
132C ASP 3.2 0.2 - - - -
133C LEU* 1.3 78.6 - - - +
135C ARG* 1.3 57.4 - - - +
137C TYR* 3.3 1.3 + - - -
138C GLY* 2.8 24.9 + - - -
139C ILE* 3.1 41.6 + - + +
141C PHE* 3.8 21.8 - - + +
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Residues in contact with ARG 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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47B ASP* 3.2 35.4 + - - +
161B ARG* 4.3 10.5 + - - +
164B ARG* 5.5 6.3 - - - +
165B LYS* 3.6 42.3 - - + +
168B GLU* 3.5 29.4 + - + +
131C GLN 2.9 12.6 + - - +
132C ASP* 2.7 56.6 + - - +
134C ALA* 1.3 76.8 - - - +
136C SER* 1.3 64.6 + - - +
138C GLY* 3.2 13.0 + - - -
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Residues in contact with SER 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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168B GLU* 5.5 5.7 + - - -
97C ARG* 4.2 5.5 + - - -
132C ASP* 3.3 13.3 + - - -
133C LEU* 3.3 12.9 + - - -
135C ARG* 1.3 82.7 + - - +
137C TYR* 1.3 72.4 + - - +
138C GLY* 3.5 0.5 + - - -
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Residues in contact with TYR 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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93C ILE* 4.1 20.0 - - + -
94C HIS* 3.0 44.5 + + - +
97C ARG* 3.5 67.4 + - + +
111C MET* 5.4 3.9 - - + +
113C LEU* 6.5 0.4 - - + -
133C LEU* 3.2 36.4 + - + +
134C ALA* 5.4 0.2 - - - -
136C SER* 1.3 85.2 - - - +
138C GLY* 1.3 61.7 + - - +
139C ILE* 3.7 39.0 - - + +
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Residues in contact with GLY 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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134C ALA 2.8 7.4 + - - -
135C ARG* 3.2 11.8 + - - -
136C SER 3.3 0.4 - - - -
137C TYR* 1.3 80.8 - - - +
139C ILE* 1.3 61.7 + - - +
140C PRO* 4.7 1.0 - - - +
162C GLU* 5.4 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