Contacts of the helix formed by residues 117 - 130 (chain C) in PDB entry 4QPL
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 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C VAL* 3.9 18.8 - - + +
45C HIS* 4.0 20.0 - - + -
58C LEU* 3.7 21.0 - - + +
115C GLN 3.6 2.2 + - - -
116C TYR* 1.3 78.3 - - - +
118C GLU* 1.3 58.7 + - - +
119C ARG* 2.9 32.9 + - - +
120C THR* 2.7 29.5 + - - -
121C SER* 2.9 25.5 + - - -
139C ILE* 5.6 1.4 - - - +
177C VAL* 4.2 1.6 - - - -
178C ALA* 4.0 14.3 - - + +
201C V3L 5.2 3.2 + - - -
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Residues in contact with GLU 118 (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 CYS 5.5 0.9 - - - +
44C VAL* 4.2 25.0 - - + +
45C HIS* 4.8 4.6 + - - +
96C ALA* 5.9 4.0 - - + +
116C TYR 3.7 0.8 + - - -
117C ASP* 1.3 73.4 - - - +
119C ARG* 1.3 66.5 + - - +
121C SER* 3.3 7.8 + - - -
122C ARG* 3.1 57.4 + - - +
177C VAL* 5.5 0.2 - - - +
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Residues in contact with ARG 119 (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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39C CYS* 4.5 2.2 - - - -
41C GLN* 3.6 33.3 + - - +
42C THR* 2.7 39.0 + - - +
44C VAL* 3.1 31.0 - - + +
56C CYS* 4.3 9.9 - - - -
117C ASP* 2.9 10.3 + - - +
118C GLU* 1.3 78.0 - - - +
120C THR* 1.3 65.1 + - - +
122C ARG* 3.3 37.2 + - - +
123C GLU* 3.4 11.4 + - - +
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Residues in contact with THR 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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116C TYR* 3.7 19.5 - - + -
117C ASP* 2.7 30.1 + - - -
119C ARG* 1.3 77.5 - - - +
121C SER* 1.3 62.1 + - - +
123C GLU* 3.2 7.9 + - + +
124C LEU* 3.0 22.4 + - + +
137C MET* 3.4 44.5 - - + +
138C LEU 4.7 4.9 + - - -
139C ILE* 4.2 12.1 - - + +
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Residues in contact with SER 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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103C TYR* 5.8 1.2 - - - -
104C ALA* 4.6 4.7 - - - +
105C TRP* 3.5 28.2 + - - +
115C GLN* 6.1 0.2 - - - +
116C TYR* 4.2 15.5 - - - +
117C ASP 2.9 18.9 + - - -
118C GLU* 3.6 9.6 - - - -
119C ARG 3.2 0.2 - - - -
120C THR* 1.3 77.1 - - - +
122C ARG* 1.3 56.1 + - - +
124C LEU* 3.4 8.0 + - - +
125C GLU* 3.0 29.3 + - - +
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Residues in contact with ARG 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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44C VAL* 5.6 0.2 - - - +
118C GLU* 3.1 50.9 + - - +
119C ARG* 3.3 38.6 + - - +
121C SER* 1.3 72.4 - - - +
123C GLU* 1.3 65.7 + - - +
125C GLU* 3.5 6.2 + - - +
126C ASP* 3.1 23.7 + - - +
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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 ARG 3.4 8.2 + - - +
120C THR* 3.2 13.4 + - + +
122C ARG* 1.3 78.3 - - - +
124C LEU* 1.3 64.8 + - + +
126C ASP* 3.2 12.1 + - - +
127C ALA* 3.0 24.9 + - - +
132C LYS* 5.0 7.3 + - - -
135C THR* 2.7 35.1 + - + +
136C GLU 4.4 11.7 - - - +
137C MET* 5.2 6.7 - - + -
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Residues in contact with LEU 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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105C TRP* 3.7 33.3 - - + -
116C TYR* 3.6 47.1 - - + -
120C THR 3.0 17.6 + - - +
121C SER* 3.7 6.1 - - - +
122C ARG 3.4 0.2 - - - -
123C GLU* 1.3 76.8 - - + +
125C GLU* 1.3 56.5 + - - +
127C ALA* 3.4 4.8 + - - +
128C PHE* 2.9 31.7 + - - +
135C THR* 4.3 7.0 - - + -
137C MET* 4.1 10.1 - - + -
146C ALA* 3.5 32.1 - - + -
148C LEU* 4.3 13.6 - - + +
165C ILE* 5.0 2.7 - - + -
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Residues in contact with GLU 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 TYR* 3.4 29.7 + - + +
105C TRP* 2.8 28.2 + - + +
121C SER 3.0 17.2 + - - +
122C ARG* 3.9 7.2 - - - +
123C GLU 3.3 0.2 - - - -
124C LEU* 1.3 75.6 - - - +
126C ASP* 1.3 57.3 + - - +
128C PHE* 5.1 4.1 - - - -
129C SER* 3.0 39.6 + - - +
167C ARG* 2.8 33.6 + - - -
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Residues in contact with ASP 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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122C ARG 3.1 18.1 + - - +
123C GLU* 3.2 14.8 + - - +
125C GLU* 1.3 77.0 - - - +
127C ALA* 1.3 63.9 + - - +
129C SER* 3.1 19.1 + - - -
130C LYS* 3.0 49.8 + - - +
132C LYS* 4.3 9.0 + - - -
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Residues in contact with ALA 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* 3.0 18.0 + - - +
124C LEU 3.7 2.2 - - - +
126C ASP* 1.3 77.7 + - - +
128C PHE* 1.3 62.5 + - - +
130C LYS 3.3 2.4 + - - -
131C GLY 3.2 3.8 + - - -
132C LYS* 3.0 47.0 + - + +
135C THR* 3.8 25.8 - - + -
148C LEU* 3.7 20.4 - - + -
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Residues in contact with PHE 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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105C TRP* 3.6 31.0 - + + -
124C LEU 2.9 18.2 + - - +
125C GLU* 3.8 6.3 - - - +
127C ALA* 1.3 77.4 - - - +
129C SER* 1.3 62.4 + - - +
131C GLY* 3.1 19.0 + - - +
132C LYS 5.1 0.7 - - - +
148C LEU* 3.8 26.2 - - + +
151C MET* 5.3 7.2 - - + -
167C ARG* 4.3 22.2 - - + -
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Residues in contact with SER 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 GLU* 3.0 23.9 + - - +
126C ASP* 3.1 17.0 + - - -
128C PHE* 1.3 81.6 - - - +
130C LYS* 1.3 62.7 + - - +
131C GLY 3.4 0.4 + - - -
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Residues in contact with LYS 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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126C ASP* 3.0 48.5 + - - +
127C ALA 3.9 3.6 - - - +
128C PHE 3.2 0.6 - - - -
129C SER* 1.3 81.4 - - - +
131C GLY* 1.3 62.1 + - - +
132C LYS* 3.5 24.6 + - + +
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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