Contacts of the helix formed by residues 126 - 137 (chain D) in PDB entry 5JKL
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D ASN* 3.2 26.1 + - - +
12D TYR* 3.6 12.8 - - - -
13D HIS 4.8 0.7 + - - +
16D SER* 4.7 3.4 + - - +
76D ARG* 2.9 32.0 + - - -
121D ALA* 3.0 17.7 + - + +
122D THR* 5.1 0.2 - - - +
124D LYS* 4.3 7.9 - - + +
125D ASN* 1.3 73.9 - - - +
127D PRO* 1.4 65.3 - - - +
128D HIS* 3.4 4.5 + - - +
129D LEU* 3.0 26.5 + - + +
130D CYS* 3.1 25.1 + - - -
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Residues in contact with PRO 127 (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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11D ASN* 4.0 7.9 - - - +
125D ASN* 3.2 14.6 - - + +
126D ASP* 1.4 82.5 - - - +
128D HIS* 1.3 65.9 + - - +
130D CYS* 3.6 9.9 - - + +
131D ASP* 3.0 25.6 + - - +
115E LEU* 3.7 22.2 - - + +
118E HIS* 3.4 45.8 - - + +
134E GLU* 4.1 5.2 - - + +
138E LEU* 3.7 11.7 - - + -
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Residues in contact with HIS 128 (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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72D LEU* 3.7 27.6 - - + +
75D GLN* 5.2 0.7 - - - -
76D ARG* 3.2 34.3 + - - +
126D ASP* 3.2 2.6 + - - +
127D PRO* 1.3 83.0 - - - +
129D LEU* 1.4 58.6 + - - +
131D ASP* 3.4 7.6 + - - +
132D PHE* 3.0 30.9 + + + +
115E LEU* 5.5 4.7 - - + -
138E LEU* 3.7 39.2 - - + +
139E ASN* 2.9 35.4 + - + -
142E VAL* 3.7 15.1 - - + +
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Residues in contact with LEU 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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12D TYR* 4.4 6.7 - - + -
16D SER* 3.9 27.8 - - - +
20D ILE* 4.0 28.7 - - + -
72D LEU* 4.3 17.5 - - + -
76D ARG* 4.1 3.4 - - - +
117D LEU* 5.1 5.6 - - + -
121D ALA* 3.8 20.9 - - + -
126D ASP* 3.0 29.1 + - + +
128D HIS* 1.4 76.5 + - - +
130D CYS* 1.3 65.1 + - - +
132D PHE* 3.3 13.1 + - + +
133D ILE* 3.0 39.9 + - + +
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Residues in contact with CYS 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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118D HIS* 3.6 23.1 - - + +
121D ALA* 3.7 7.2 - - - -
122D THR* 3.6 39.9 - - - -
126D ASP 3.1 20.1 + - - +
127D PRO* 3.6 12.3 - - + +
128D HIS 3.4 0.2 - - - -
129D LEU* 1.3 75.5 - - - +
131D ASP* 1.3 57.1 + - - +
133D ILE* 3.3 3.7 + - - +
134D GLU* 3.0 39.1 + - - +
134E GLU* 5.6 3.1 - - - +
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Residues in contact with ASP 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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127D PRO 3.0 18.5 + - - +
128D HIS* 3.7 8.7 - - - +
130D CYS* 1.3 73.5 - - - +
132D PHE* 1.3 59.8 + - - +
134D GLU* 4.4 6.0 + - - -
135D THR* 2.7 55.8 + - - +
134E GLU* 3.6 44.2 + - + +
135E THR* 4.5 3.3 + - - -
138E LEU* 6.0 1.2 - - + +
139E ASN* 5.0 9.7 + - - +
202E MG 3.5 15.6 - - - -
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Residues in contact with PHE 132 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D ILE* 5.2 0.2 - - + -
68D LYS* 3.8 28.0 - - + -
69D LEU* 3.7 19.1 - - + -
72D LEU* 3.7 46.0 - - + -
75D GLN* 5.3 2.9 - - - -
128D HIS* 3.0 18.5 + + + +
129D LEU* 3.3 16.1 + - + +
131D ASP* 1.3 79.3 + - - +
133D ILE* 1.3 74.6 + - + +
136D HIS* 3.1 46.4 + + - +
137D TYR* 3.5 30.5 - + - -
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Residues in contact with ILE 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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69D LEU* 6.3 0.2 - - + -
114D LEU* 4.2 14.8 - - + +
117D LEU* 3.7 38.1 - - + +
118D HIS* 4.0 27.6 - - + -
121D ALA* 4.8 0.4 - - + -
129D LEU* 3.0 30.9 + - + +
130D CYS* 3.7 3.4 - - - +
132D PHE* 1.3 87.2 - - + +
134D GLU* 1.3 58.3 + - - +
137D TYR* 2.9 35.9 + - + +
138D LEU* 3.0 34.6 + - + -
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Residues in contact with GLU 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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118D HIS* 2.7 34.0 + - + +
130D CYS* 3.0 24.7 + - - +
131D ASP* 3.8 5.8 + - - +
133D ILE* 1.3 78.7 - - - +
135D THR* 1.3 62.9 + - - +
138D LEU* 3.9 25.8 + - + +
139D ASN* 4.2 9.2 + - - +
203D MG 3.7 18.9 - - - -
134E GLU* 4.4 6.3 - - - +
127F PRO* 4.2 7.6 - - - +
130F CYS* 5.7 1.7 - - - +
131F ASP* 3.5 48.1 + - + +
134F GLU* 4.4 8.0 - - - +
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Residues in contact with THR 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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131D ASP* 2.7 45.7 + - - +
134D GLU* 1.3 76.4 - - - +
136D HIS* 1.3 86.7 + - + +
139D ASN* 5.8 2.4 - - - +
140D GLU* 5.6 2.1 - - - +
131F ASP* 4.8 7.6 + - - -
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Residues in contact with HIS 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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65D HIS* 5.4 4.5 - - - -
68D LYS* 3.3 31.7 + - + +
132D PHE* 3.1 41.1 + + - +
135D THR* 1.3 102.2 + - + +
137D TYR* 1.3 77.4 + - + +
139D ASN 5.6 0.2 - - - -
140D GLU* 3.4 22.5 - - - +
139E ASN* 6.0 1.8 + - - -
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Residues in contact with TYR 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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27D GLU* 4.1 8.1 - - - -
65D HIS* 2.7 54.5 + + + -
68D LYS* 3.3 20.6 - - + +
69D LEU* 3.4 22.1 - - + +
114D LEU* 3.9 35.7 - - + -
132D PHE* 3.5 34.3 - + - -
133D ILE* 2.9 16.2 + - + +
135D THR 3.7 0.6 - - - -
136D HIS* 1.3 96.6 - - + +
138D LEU* 1.3 66.0 + - - +
139D ASN 3.4 2.0 - - - -
140D GLU* 3.2 6.0 + - - +
141D GLN* 3.0 28.9 + - - +
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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