Contacts of the helix formed by residues 128 - 139 (chain C) in PDB entry 5EJK
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 SER 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C SER* 2.9 28.4 + - - -
124C SER 3.4 13.4 + - - -
125C CYS 3.9 1.2 + - - -
126C PHE 4.6 0.2 - - - +
127C THR* 1.3 81.5 - - - +
129C LYS* 1.3 60.0 + - - +
130C SER* 4.2 2.5 - - - -
131C THR* 2.6 43.4 + - - +
132C ARG* 3.0 17.0 + - - +
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Residues in contact with LYS 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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127C THR 3.9 1.0 + - - -
128C SER* 1.3 71.5 - - - +
130C SER* 1.3 60.4 + - - +
132C ARG* 3.1 30.9 + - - +
133C GLU* 2.9 53.4 + - + +
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Residues in contact with SER 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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98C SER* 4.4 15.6 - - - -
99C VAL* 6.1 0.9 - - - +
102C GLN* 3.1 20.0 + - - +
128C SER* 3.3 2.3 + - - -
129C LYS* 1.3 77.7 - - - +
131C THR* 1.3 56.3 + - - +
133C GLU* 3.2 11.7 + - - +
134C TRP* 2.9 23.7 + - - +
137C ARG* 4.6 3.5 + - - -
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Residues in contact with THR 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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98C SER* 3.4 19.5 - - - +
101C VAL* 4.7 7.0 - - + -
102C GLN* 3.3 22.7 - - + +
105C TRP* 4.8 9.8 - - + -
125C CYS 3.2 23.8 + - - +
126C PHE 3.7 9.1 + - - -
128C SER* 2.6 37.5 + - - +
130C SER* 1.3 75.5 - - - +
132C ARG* 1.3 56.0 + - - +
134C TRP* 3.2 4.5 + - - +
135C MSE 2.9 34.7 + - - +
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Residues in contact with ARG 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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126C PHE 5.8 1.8 - - - +
127C THR 3.8 18.6 + - - -
128C SER 3.0 14.2 + - - +
129C LYS* 3.1 48.7 + - - +
131C THR* 1.3 77.0 + - - +
133C GLU* 1.3 58.4 + - - +
135C MSE 3.1 11.1 + - + +
136C ALA* 2.9 27.7 + - + +
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Residues in contact with GLU 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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129C LYS* 2.9 48.3 + - + +
130C SER* 3.2 9.6 + - - +
132C ARG* 1.3 77.5 - - + +
134C TRP* 1.3 57.4 + - - +
136C ALA* 3.2 7.7 + - - +
137C ARG* 2.9 58.6 + - + +
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Residues in contact with TRP 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLN* 3.3 43.7 - - + +
105C TRP* 3.5 46.7 - + + -
106C ALA* 3.9 13.5 - - + -
109C ILE* 3.7 19.1 - - + -
118C ILE* 6.1 0.9 - - + -
130C SER 2.9 13.8 + - - +
131C THR 3.5 7.6 - - - +
133C GLU* 1.3 77.7 - - - +
135C MSE 1.3 70.3 + - - +
137C ARG* 3.7 18.7 + - - +
138C TRP* 3.1 57.8 + + + +
140C ILE* 5.0 3.4 - - + -
187D GLU* 2.9 31.2 + - - +
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Residues in contact with MSE 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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105C TRP* 3.6 37.5 - - + -
118C ILE* 4.7 6.7 - - + -
126C PHE 6.2 0.4 - - - +
131C THR* 2.9 21.4 + - - +
132C ARG* 3.4 11.0 - - + +
134C TRP* 1.3 83.1 - - - +
136C ALA* 1.3 64.7 + - - +
138C TRP* 3.4 3.6 + - - +
139C GLY* 3.2 17.3 + - - -
140C ILE* 3.2 58.1 + - + +
141C ALA 3.2 20.9 - - - +
142C HIS* 3.6 24.9 - - + -
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Residues in contact with ALA 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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132C ARG* 2.9 14.6 + - + +
133C GLU* 3.2 11.6 + - - +
135C MSE 1.3 78.1 - - - +
137C ARG* 1.3 62.8 - - + +
138C TRP 3.2 0.9 + - - -
139C GLY* 3.2 12.9 + - - -
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Residues in contact with ARG 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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102C GLN* 4.9 3.4 - - - +
130C SER* 4.6 3.4 + - - -
133C GLU* 2.9 45.9 + - + +
134C TRP* 3.7 36.8 - - - +
136C ALA* 1.3 77.4 - - + +
138C TRP* 1.3 64.5 + - + +
184D LYS* 5.7 4.8 - - - +
187D GLU* 5.4 0.6 + - - -
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Residues in contact with TRP 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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106C ALA* 5.7 4.9 - - + -
109C ILE* 4.1 26.0 - - + -
114C ARG* 3.7 38.3 + - + -
134C TRP* 3.1 66.8 + + + +
135C MSE 3.4 3.2 + - - +
136C ALA 3.1 0.8 - - - -
137C ARG* 1.3 84.7 - - + +
139C GLY* 1.3 63.7 + - - +
140C ILE* 3.5 21.1 - - + +
12D LEU* 5.0 6.3 - - + -
190D ALA* 5.9 2.0 - - + -
191D LYS* 4.1 38.9 - - + +
194D TYR* 4.1 33.0 - + + -
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Residues in contact with GLY 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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114C ARG* 5.2 1.4 + - - -
115C PRO 4.6 0.3 - - - +
116C LYS* 4.0 20.6 - - - +
135C MSE 3.2 5.3 + - - -
136C ALA* 3.2 11.2 + - - -
137C ARG 3.5 0.4 - - - -
138C TRP* 1.3 79.1 - - - +
140C ILE* 1.3 60.6 + - - +
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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