Contacts of the helix formed by residues 117 - 128 (chain C) in PDB entry 4UQJ
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 LEU 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C PRO 3.3 4.9 + - - +
116C ASP* 1.3 71.4 + - - +
118C LYS* 1.3 66.9 + - - +
119C GLY 3.1 3.4 - - - -
120C ALA* 3.0 12.7 + - + -
121C LEU* 2.9 27.0 + - + +
145C THR* 5.3 7.4 - - + -
223C ALA* 3.5 38.6 - - + +
224C ASN* 3.5 14.4 - - - +
225C LEU* 3.8 25.1 - - + +
245C PHE* 3.6 39.5 - - + -
358C ILE* 4.2 5.2 - - + -
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Residues in contact with LYS 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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116C ASP* 3.3 22.7 + - - +
117C LEU* 1.3 78.0 - - - +
119C GLY* 1.3 61.1 + - - +
121C LEU* 3.6 5.5 + - - +
122C LEU* 3.3 31.6 + - + +
144C SER* 5.5 3.8 - - - +
145C THR* 4.5 22.7 - - + +
148C ALA* 4.5 17.4 - - + +
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Residues in contact with GLY 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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116C ASP* 4.2 5.9 + - - -
117C LEU 3.0 1.4 + - - -
118C LYS* 1.3 76.3 - - - +
120C ALA* 1.3 64.9 + - - +
121C LEU 3.3 0.2 + - - -
122C LEU* 3.4 8.1 + - - +
123C SER* 3.1 26.3 + - - -
374C TRP* 3.5 22.0 - - - -
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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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117C LEU* 3.0 18.8 + - + +
119C GLY* 1.3 76.3 - - - +
121C LEU* 1.3 60.9 + - - +
123C SER* 3.6 2.1 + - - -
124C LEU* 3.2 17.8 + - - +
245C PHE* 3.4 28.6 - - + -
358C ILE* 4.1 9.2 - - + -
374C TRP* 3.6 42.3 - - + +
380C MET* 4.6 1.4 - - - +
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Residues in contact with LEU 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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117C LEU* 2.9 20.0 + - + +
118C LYS* 3.8 6.1 - - - +
120C ALA* 1.3 74.5 - - - +
122C LEU* 1.3 67.5 + - + +
124C LEU* 3.0 14.0 + - + +
125C ILE* 3.1 36.7 + - + +
135C TYR* 4.5 20.0 - - + +
145C THR* 5.1 11.9 - - + -
149C VAL* 4.7 10.8 - - + -
193C ILE* 4.1 13.5 - - + -
221C ILE* 5.0 5.6 - - + -
223C ALA* 3.9 24.5 - - + -
245C PHE* 3.6 24.3 - - + -
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LYS* 3.3 18.9 + - + +
119C GLY* 3.9 6.3 - - - +
121C LEU* 1.3 79.0 - - + +
123C SER* 1.3 61.3 + - - +
125C ILE* 3.4 9.5 + - + +
126C GLU* 3.4 26.3 + - - +
148C ALA* 4.2 14.6 - - + +
149C VAL* 3.9 34.8 - - + +
152C SER* 3.4 30.1 - - - +
158C TRP* 4.3 13.3 - - + -
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Residues in contact with SER 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 GLY 3.1 8.7 + - - -
120C ALA 3.8 0.9 - - - -
121C LEU 3.1 0.8 - - - -
122C LEU* 1.3 75.0 - - - +
124C LEU* 1.3 65.5 + - - +
126C GLU* 3.4 9.4 + - - +
127C TYR* 3.1 20.6 + - - +
374C TRP* 2.8 41.1 + - - -
379C LYS* 4.5 7.2 - - - +
380C MET* 4.1 14.2 - - - +
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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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120C ALA 3.2 11.6 + - - +
121C LEU* 3.0 9.1 + - + +
123C SER* 1.3 75.9 - - - +
125C ILE* 1.3 66.7 + - + +
127C TYR* 3.1 13.3 + - + +
128C TYR* 3.2 53.2 + - + -
221C ILE* 3.9 24.0 - - + -
243C SER* 4.4 9.9 - - - -
244C GLY 4.8 5.6 - - - +
245C PHE* 3.6 24.7 - - + -
360C ILE* 3.8 19.1 - - + -
380C MET* 3.4 27.3 - - + +
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Residues in contact with ILE 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 LEU* 3.1 34.4 + - + +
122C LEU* 3.6 10.8 - - - +
123C SER 3.3 0.4 - - - -
124C LEU* 1.3 77.5 - - - +
126C GLU* 1.3 57.4 + - - +
128C TYR* 3.5 3.7 + - - -
129C GLN 3.1 20.1 + - - -
130C TRP* 3.1 39.7 + - + +
133C PHE* 3.7 20.9 - - + -
149C VAL* 4.6 7.6 - - + -
158C TRP* 3.7 32.5 - - + -
193C ILE* 3.7 22.9 - - + -
221C ILE* 5.0 6.3 - - + -
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Residues in contact with GLU 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 LEU 3.4 11.4 + - - +
123C SER* 3.4 11.7 + - - +
124C LEU 3.3 0.2 - - - -
125C ILE* 1.3 74.6 - - - +
127C TYR* 1.3 65.8 + - - +
129C GLN* 2.9 23.0 + - - +
130C TRP 5.0 0.9 - - - +
156C LYS* 4.8 8.5 - - + +
158C TRP* 4.1 20.9 - - + -
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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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123C SER 3.1 13.8 + - - +
124C LEU* 3.1 10.3 + - + +
126C GLU* 1.3 77.8 - - - +
128C TYR* 1.3 98.5 + + - +
129C GLN* 3.3 10.2 + - - +
362C GLU* 4.7 1.9 + - - -
371C ILE* 4.4 17.6 - - + +
380C MET* 3.8 25.8 - - - -
382C LEU* 3.5 40.6 - - + +
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Residues in contact with TYR 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 LEU* 3.2 49.8 + - + +
125C ILE* 4.1 0.9 - - - +
127C TYR* 1.3 93.1 - + - +
129C GLN* 1.3 72.3 + - - +
130C TRP* 3.2 28.1 + - + +
191C ARG* 4.5 5.0 + - - -
219C HIS* 3.8 25.1 - + - -
221C ILE* 4.4 9.0 - - + -
241C GLU* 5.2 2.7 - - - -
243C SER* 2.7 30.2 + - - -
360C ILE* 4.9 0.2 - - - +
362C GLU* 2.7 29.1 + - - +
371C ILE* 4.0 5.4 - - - +
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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