Contacts of the helix formed by residues 126 - 137 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11K ASN* 3.3 24.8 + - - +
12K TYR* 3.7 12.0 - - - -
13K HIS 4.8 1.0 + - - +
16K SER* 4.7 3.9 + - - +
76K ARG* 2.9 32.3 + - - -
121K ALA* 2.9 17.7 + - + +
122K THR* 5.2 0.2 - - - +
124K LYS* 4.4 7.6 - - + +
125K ASN* 1.4 73.5 - - - +
127K PRO* 1.3 64.9 - - - +
128K HIS* 3.5 4.0 + - - +
129K LEU* 3.1 25.7 + - + +
130K CYS* 3.1 25.6 + - - -
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Residues in contact with PRO 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K ASN* 4.0 8.5 - - - +
125K ASN 3.2 14.1 - - - +
126K ASP* 1.3 86.6 - - - +
128K HIS* 1.3 58.8 + - - +
130K CYS* 3.5 10.4 - - + +
131K ASP* 2.9 30.5 + - - +
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Residues in contact with HIS 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K LEU* 3.8 26.4 - - + +
75K GLN* 5.3 5.8 - - + -
76K ARG* 3.2 35.7 + - - +
126K ASP* 3.2 2.7 + - - +
127K PRO* 1.3 81.9 - - - +
129K LEU* 1.3 57.8 + - - +
131K ASP* 3.3 13.2 + - - +
132K PHE* 2.9 32.3 + + + +
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Residues in contact with LEU 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K TYR* 4.4 6.5 - - + -
16K SER* 3.9 26.7 - - - -
20K ILE* 3.8 29.6 - - + -
72K LEU* 4.2 16.8 - - + -
76K ARG* 4.0 3.6 - - - +
117K LEU* 5.0 5.4 - - + -
121K ALA* 3.8 20.4 - - + -
126K ASP* 3.1 30.2 + - + +
128K HIS* 1.3 76.1 + - - +
130K CYS* 1.3 65.1 + - - +
132K PHE* 3.2 11.0 + - + +
133K ILE* 3.0 42.5 + - + +
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Residues in contact with CYS 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118K HIS* 3.6 24.2 + - + +
121K ALA* 3.7 17.7 - - - -
122K THR* 3.5 30.3 - - - -
126K ASP 3.1 19.4 + - - -
127K PRO* 3.5 12.3 - - + +
129K LEU* 1.3 74.5 - - - +
131K ASP* 1.3 63.0 + - - +
133K ILE* 3.3 0.6 + - - -
134K GLU* 3.0 35.1 + - - +
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Residues in contact with ASP 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K PRO 2.9 19.1 + - - +
128K HIS* 3.6 13.2 + - + +
130K CYS* 1.3 75.2 - - - +
132K PHE* 1.3 57.2 + - - +
134K GLU* 3.4 9.7 + - - +
135K THR* 2.8 55.5 + - - -
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Residues in contact with PHE 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K LYS* 3.8 24.9 - - + -
69K LEU* 3.6 19.1 - - + -
72K LEU* 3.8 44.0 - - + -
75K GLN* 5.3 3.6 - - - -
128K HIS* 2.9 22.1 + + + +
129K LEU* 3.2 13.2 + - + +
131K ASP* 1.3 79.4 + - - +
133K ILE* 1.3 73.2 + - + +
136K HIS* 3.1 49.4 + + - +
137K TYR* 3.2 34.8 - + - -
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Residues in contact with ILE 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K LEU* 4.1 14.6 - - + +
117K LEU* 3.6 37.5 - - + +
118K HIS* 3.9 28.5 - - + +
121K ALA* 4.7 0.4 - - + -
129K LEU* 3.0 30.8 + - + +
130K CYS* 3.7 4.3 - - - +
132K PHE* 1.3 89.1 - - + +
134K GLU* 1.3 57.4 + - - +
137K TYR* 3.0 19.7 + - + +
138K LEU* 2.9 48.3 + - + -
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Residues in contact with GLU 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118K HIS* 2.7 32.4 + - - +
130K CYS* 3.0 25.0 + - - +
131K ASP* 3.7 9.1 - - - +
133K ILE* 1.3 76.0 - - - +
135K THR* 1.3 65.3 + - - +
138K LEU* 3.9 29.3 + - + +
139K ASN* 4.2 10.7 + - - +
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Residues in contact with THR 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131K ASP* 2.8 44.5 + - - +
134K GLU* 1.3 77.3 - - - +
136K HIS* 1.3 87.6 + - + +
139K ASN* 5.7 3.1 + - - +
140K GLU* 5.5 2.9 + - - +
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Residues in contact with HIS 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65K HIS* 5.5 3.5 + - - -
68K LYS* 3.1 35.6 + - + +
132K PHE* 3.1 44.2 + + - +
135K THR* 1.3 100.5 + - + +
137K TYR* 1.3 78.4 + - + +
140K GLU* 3.3 22.8 - - - +
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Residues in contact with TYR 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K GLU* 4.1 14.1 - - - -
65K HIS* 2.7 53.9 + + + -
68K LYS* 3.3 20.2 - - + +
69K LEU* 3.4 21.2 + - + +
114K LEU* 3.9 29.2 - - + -
132K PHE* 3.2 38.1 - + - -
133K ILE* 3.0 12.1 + - + +
135K THR 3.6 0.8 - - - -
136K HIS* 1.3 96.6 - - + +
138K LEU* 1.3 68.4 + - - +
139K ASN 3.4 1.8 - - - +
140K GLU* 3.3 6.4 + - - +
141K GLN* 3.0 27.4 + - - +
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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