Contacts of the helix formed by residues 137 - 159 (chain G) 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 TYR 137 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G GLU* 4.1 13.9 - - - -
65G HIS* 2.7 49.0 + + + -
68G LYS* 3.4 18.1 - - + +
69G LEU* 3.2 27.9 + - + +
114G LEU* 3.8 30.1 - - + -
132G PHE* 3.4 35.7 - + - -
133G ILE* 2.9 17.2 + - + +
135G THR 3.7 0.4 - - - -
136G HIS* 1.3 95.7 - - + +
138G LEU* 1.3 66.7 + - - +
139G ASN 3.4 1.8 - - - +
140G GLU* 3.3 5.9 + - - +
141G GLN* 2.9 28.1 + - - +
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Residues in contact with LEU 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G ASN* 4.3 7.6 - - - +
114G LEU* 3.9 22.0 - - + -
115G LEU* 4.2 28.0 - - + -
118G HIS* 4.4 13.2 - - + -
133G ILE* 3.0 33.6 + - + +
134G GLU* 3.9 28.2 + - + +
137G TYR* 1.3 75.1 - - - +
139G ASN* 1.4 59.1 + - - +
141G GLN* 3.4 5.9 + - - +
142G VAL* 3.1 30.5 + - + +
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Residues in contact with ASN 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G GLU 4.1 8.9 + - - +
135G THR 5.7 2.7 + - - +
136G HIS 5.5 0.2 - - - -
137G TYR 3.4 0.4 - - - +
138G LEU* 1.4 77.4 - - - +
140G GLU* 1.3 67.8 + - - +
142G VAL* 4.1 17.2 - - - +
143G LYS* 3.0 50.5 + - - +
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Residues in contact with GLU 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G GLU* 4.5 13.1 - - - +
65G HIS* 4.9 19.3 + - + +
135G THR 5.5 2.0 - - - +
136G HIS* 3.4 26.0 - - - +
137G TYR* 3.5 7.8 - - - +
138G LEU 3.3 0.2 - - - -
139G ASN* 1.3 81.7 + - - +
141G GLN* 1.3 59.6 + - - +
143G LYS* 3.0 34.5 + - - +
144G ALA* 3.0 28.8 + - - +
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Residues in contact with GLN 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G HIS* 4.7 6.2 - - - -
107G GLU* 2.7 53.8 + - - +
110G VAL* 3.8 17.9 - - - +
111G ASN* 3.5 26.2 - - + +
114G LEU* 3.4 27.0 - - + +
137G TYR* 2.9 13.2 + - - +
138G LEU 3.6 5.2 - - - +
140G GLU* 1.3 76.8 - - - +
142G VAL* 1.3 65.1 + - - +
144G ALA* 3.2 3.9 + - - +
145G ILE* 3.0 30.2 + - + +
201G FE 3.9 14.7 - - - -
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Residues in contact with VAL 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G ASN* 4.9 13.0 - - - +
138G LEU* 3.1 20.7 + - + +
139G ASN* 3.3 16.4 + - - +
141G GLN* 1.3 76.1 - - - +
143G LYS* 1.3 65.2 + - + +
145G ILE* 3.5 6.8 + - + +
146G LYS* 3.0 26.4 + - + +
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Residues in contact with LYS 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G ASN* 3.0 41.3 + - - +
140G GLU* 3.0 37.2 + - - +
142G VAL* 1.3 78.0 - - + +
144G ALA* 1.3 57.1 + - - +
146G LYS* 3.4 6.5 + - - +
147G GLU* 3.0 28.8 + - - +
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Residues in contact with ALA 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G GLN* 5.8 3.8 - - - +
61G GLU* 5.6 5.4 - - - +
107G GLU* 4.3 25.6 - - + +
140G GLU 3.0 18.6 + - - +
141G GLN* 3.2 6.0 + - - +
143G LYS* 1.3 73.7 - - - +
145G ILE* 1.4 58.6 + - - +
147G GLU* 3.3 6.8 + - - +
148G LEU* 2.9 38.4 + - + +
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Residues in contact with ILE 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G LEU* 3.8 22.3 - - + +
107G GLU* 3.8 30.3 - - + +
108G LYS* 3.9 31.0 - - + -
111G ASN* 3.9 27.1 - - + +
141G GLN* 3.0 20.9 + - + +
142G VAL* 3.9 7.0 - - + +
144G ALA* 1.4 73.1 - - - +
146G LYS* 1.3 57.8 + - - +
148G LEU* 3.4 2.8 + - - -
149G GLY* 2.9 26.9 + - - -
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Residues in contact with LYS 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G VAL* 3.0 22.2 + - + +
143G LYS* 3.8 6.1 - - - +
145G ILE* 1.3 77.1 - - - +
147G GLU* 1.3 56.8 + - - +
149G GLY* 3.4 2.2 + - - +
150G ASP* 2.8 66.9 + - - +
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Residues in contact with GLU 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G TYR* 2.6 33.5 + - - +
58G GLN* 4.2 6.2 + - - -
143G LYS 3.0 17.7 + - - +
144G ALA* 3.6 7.4 - - - +
145G ILE 3.3 0.2 - - - -
146G LYS* 1.3 78.7 - - - +
148G LEU* 1.3 57.3 + - - +
150G ASP* 3.2 11.0 + - - +
151G HIS* 2.9 50.4 + - + +
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Residues in contact with LEU 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G TYR* 3.9 7.6 - - - +
54G TYR* 3.8 21.8 - - + +
100G MET* 3.7 30.7 - - - +
103G ALA* 3.7 29.4 - - + +
104G LEU* 3.8 16.6 - - + +
107G GLU* 3.6 31.4 - - + -
144G ALA* 2.9 22.5 + - + +
145G ILE* 3.9 3.4 - - - +
147G GLU* 1.3 74.9 - - - +
149G GLY* 1.3 56.3 + - - +
151G HIS* 3.2 5.1 + - - +
152G VAL* 2.9 34.7 + - - +
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Residues in contact with GLY 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G LEU* 4.3 13.7 - - - +
145G ILE 2.9 16.7 + - - -
146G LYS* 3.7 1.6 - - - -
148G LEU* 1.3 74.7 - - - +
150G ASP* 1.3 63.1 + - - +
152G VAL* 3.4 6.4 + - - +
153G THR* 2.9 28.7 + - - -
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Residues in contact with ASP 150 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G LYS* 2.8 58.2 + - - +
147G GLU* 3.2 11.8 + - - +
149G GLY* 1.3 77.4 - - - +
151G HIS* 1.3 67.1 + - + +
153G THR* 3.3 5.5 + - - -
154G ASN* 2.9 37.2 + - - +
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Residues in contact with HIS 151 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G TYR* 3.7 21.7 + + - -
100G MET* 3.9 32.3 - - + -
147G GLU* 2.9 39.7 + - + +
148G LEU* 3.6 7.0 - - - +
150G ASP* 1.3 78.0 - - + +
152G VAL* 1.3 65.9 + - - +
154G ASN* 3.3 2.9 + - - +
155G LEU* 2.9 30.8 + - - +
170G PHE* 3.6 21.2 - + + -
174G THR* 3.7 24.0 - - + +
175G LEU* 3.8 12.0 - - + +
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Residues in contact with VAL 152 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G LEU* 3.9 13.2 - - + +
100G MET* 3.8 34.5 - - + +
101G GLU* 3.9 12.3 - - + +
104G LEU* 4.6 11.4 - - + -
148G LEU 2.9 23.0 + - - +
149G GLY* 3.8 6.3 - - - +
151G HIS* 1.3 71.1 - - - +
153G THR* 1.3 64.0 + - - +
155G LEU* 3.3 2.1 + - - +
156G ARG* 2.9 67.9 + - - +
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Residues in contact with THR 153 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149G GLY 2.9 18.8 + - - -
150G ASP* 3.6 7.4 - - - +
151G HIS 3.3 0.2 - - - -
152G VAL* 1.3 78.1 - - - +
154G ASN* 1.3 62.0 + - - +
156G ARG* 3.4 13.3 + - - +
157G LYS* 2.9 56.2 + - + +
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Residues in contact with ASN 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150G ASP* 2.9 34.0 + - - +
151G HIS* 3.9 1.0 + - - +
153G THR* 1.3 80.8 - - - +
155G LEU* 1.3 65.8 + - - +
157G LYS* 3.3 7.3 + - - +
158G MET* 2.9 36.3 + - - +
170G PHE* 3.8 24.4 - - + -
174G THR* 5.7 1.8 - - - -
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Residues in contact with LEU 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G PHE* 4.1 11.0 - - + -
97G LEU* 3.9 33.4 - - + +
100G MET* 3.9 21.3 - - + -
151G HIS 2.9 21.2 + - - +
152G VAL 3.8 3.1 - - - +
154G ASN* 1.3 78.3 - - - +
156G ARG* 1.3 61.3 + - - +
158G MET* 3.3 6.5 + - - +
159G GLY 3.3 4.5 + - - -
160G ALA* 2.9 34.4 + - + +
166G ALA 4.5 2.2 - - - +
167G GLU* 4.1 27.4 - - + -
170G PHE* 3.6 39.5 - - + -
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Residues in contact with ARG 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G LEU* 4.1 16.7 - - + +
101G GLU* 2.9 29.9 + - - +
104G LEU* 6.1 1.4 - - - +
152G VAL* 2.9 40.5 + - - +
153G THR* 3.7 11.3 + - - +
155G LEU* 1.3 74.8 - - - +
157G LYS* 1.3 64.8 + - + +
159G GLY* 3.0 15.4 + - - -
160G ALA 4.2 8.9 - - - +
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Residues in contact with LYS 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G THR* 2.9 39.6 + - + +
154G ASN* 3.9 6.3 - - - +
156G ARG* 1.3 78.2 - - + +
158G MET* 1.3 60.2 + - + +
159G GLY 3.5 0.7 + - - -
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Residues in contact with MET 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ASN* 2.9 31.9 + - + +
155G LEU* 3.7 4.9 - - - +
156G ARG 3.1 0.6 - - - -
157G LYS* 1.3 77.9 - - + +
159G GLY* 1.3 57.5 + - - +
160G ALA 3.7 0.2 - - - -
163G SER* 4.4 4.3 + - - -
166G ALA* 3.4 45.9 - - + +
169G LEU* 4.0 14.8 - - + -
170G PHE* 3.7 37.2 - - + +
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Residues in contact with GLY 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G ARG 3.0 11.1 + - - -
157G LYS 3.3 1.4 - - - -
158G MET* 1.3 79.6 - - - +
160G ALA* 1.3 67.2 + - - +
162G GLU* 3.5 5.4 + - - +
163G SER* 3.0 27.9 + - - -
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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
------------------------------------------------------------
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