Contacts of the helix formed by residues 128 - 138 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D SER* 3.4 23.9 + - - -
124D SER 4.9 6.4 + - - -
125D CYS 4.3 1.7 + - - -
126D PHE 3.3 1.4 - - - -
127D THR* 1.3 81.9 + - - +
129D LYS* 1.3 60.1 + - - +
130D SER* 3.8 6.1 + - - -
131D THR* 2.7 32.7 + - - -
132D ARG* 3.0 26.8 + - - +
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Residues in contact with LYS 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D THR 3.8 0.8 + - - -
128D SER* 1.3 70.8 - - - +
130D SER* 1.3 61.4 + - - +
132D ARG* 3.8 9.1 - - + +
133D GLU* 2.9 58.1 + - + +
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Residues in contact with SER 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D SER* 5.4 5.3 - - - -
99D VAL* 5.8 2.9 - - - +
102D GLN* 2.4 35.2 + - - +
128D SER* 3.2 8.1 + - - -
129D LYS* 1.3 78.4 - - - +
131D THR* 1.3 56.5 + - - +
133D GLU* 3.6 5.4 + - - +
134D TRP* 2.9 23.9 + - - +
137D ARG* 5.4 0.3 + - - -
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Residues in contact with THR 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D SER* 3.9 13.5 + - - -
101D VAL* 4.6 5.6 - - + +
102D GLN* 3.9 8.2 - - + +
105D TRP* 3.8 29.2 - - + -
125D CYS 3.5 10.6 + - - -
126D PHE* 3.3 28.7 - - - +
128D SER* 2.7 24.1 + - - -
130D SER* 1.3 77.9 - - - +
132D ARG* 1.3 57.4 + - - +
134D TRP* 3.3 4.4 + - + +
135D MSE 2.9 36.9 + - + +
142D HIS* 5.2 1.6 - - + -
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Residues in contact with ARG 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE 4.8 2.9 - - - +
127D THR* 3.6 41.5 + - - +
128D SER 3.0 16.1 + - - +
129D LYS* 3.8 8.7 - - + +
131D THR* 1.3 74.4 - - - +
133D GLU* 1.3 62.3 + - + +
135D MSE 3.1 9.9 + - - +
136D ALA* 2.9 28.3 + - - +
142D HIS* 4.0 24.9 + - - +
144D THR* 4.0 14.3 - - - +
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Residues in contact with GLU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D LYS* 2.9 48.0 + - + +
130D SER* 4.1 5.2 - - - +
132D ARG* 1.3 75.1 - - + +
134D TRP* 1.3 56.7 + - - +
136D ALA* 3.8 7.1 - - - +
137D ARG* 2.9 49.2 + - - +
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Residues in contact with TRP 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C GLU* 3.3 21.4 + - - -
102D GLN* 3.2 63.0 - - + +
105D TRP* 3.9 40.4 - + + -
106D ALA* 4.0 14.8 - - + -
109D ILE* 4.2 7.2 - - + -
118D ILE* 5.7 2.0 - - + -
130D SER 2.9 20.3 + - - +
131D THR 3.4 5.6 - - - +
133D GLU* 1.3 78.5 - - - +
135D MSE 1.3 70.4 + - - +
137D ARG* 3.4 28.0 + - - +
138D TRP* 3.3 51.5 - + + +
140D ILE* 5.5 5.2 - - + -
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Residues in contact with MSE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D TRP* 3.5 37.0 - - + -
118D ILE* 4.3 13.2 - - + -
131D THR* 2.9 21.6 + - + +
132D ARG* 3.1 7.8 + - - +
134D TRP* 1.3 85.8 - - - +
136D ALA* 1.3 62.1 + - - +
138D TRP* 3.3 12.0 + - - +
140D ILE* 3.3 62.5 + - + +
141D ALA 3.6 9.6 - - - +
142D HIS* 3.6 40.4 - - + +
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Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ARG 2.9 15.2 + - - +
133D GLU* 3.8 7.9 - - - +
135D MSE 1.3 77.1 - - - +
137D ARG* 1.3 62.4 + - - +
139D GLY* 3.3 13.2 + - - +
140D ILE 5.0 1.1 - - - -
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Residues in contact with ARG 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C ASP* 6.1 0.7 - - - -
187C GLU* 5.7 0.8 + - - -
191C LYS* 5.9 5.2 - - - +
130D SER 5.7 0.2 + - - -
133D GLU* 2.9 39.1 + - - +
134D TRP* 3.4 47.8 - - - +
135D MSE 3.2 0.8 - - - -
136D ALA* 1.3 77.5 - - - +
138D TRP* 1.3 66.3 + - + +
139D GLY 3.8 0.3 + - - -
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Residues in contact with TRP 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 5.6 5.4 - - + -
187C GLU* 4.9 2.9 + - - -
191C LYS* 3.8 42.8 - - + -
194C TYR* 4.3 29.6 - + + -
106D ALA* 5.8 2.0 - - + -
109D ILE* 3.5 32.3 - - + -
114D ARG* 4.1 29.9 + - + -
134D TRP* 3.3 57.3 - + + +
135D MSE 3.3 6.0 + - - +
136D ALA 3.2 0.6 - - - -
137D ARG* 1.3 86.9 - - + +
139D GLY* 1.3 63.1 + - - +
140D ILE* 3.3 26.7 + - + +
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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