Contacts of the helix formed by residues 137 - 159 (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 TYR 137 (chain K).
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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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Residues in contact with LEU 138 (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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111K ASN* 4.2 7.6 - - - +
114K LEU* 3.9 23.3 - - + -
115K LEU* 4.0 27.8 - - + -
118K HIS* 4.4 8.7 - - + -
133K ILE* 2.9 35.6 + - + +
134K GLU* 3.9 30.4 + - + +
137K TYR* 1.3 75.5 - - - +
139K ASN* 1.3 59.4 + - - +
141K GLN* 3.3 5.6 + - - +
142K VAL* 3.1 31.0 + - + +
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Residues in contact with ASN 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134K GLU 4.2 8.8 + - - +
135K THR 5.7 3.5 + - - +
136K HIS 5.6 0.2 - - - -
137K TYR 3.4 0.6 - - - +
138K LEU* 1.3 75.1 - - - +
140K GLU* 1.3 62.4 + - - +
142K VAL* 3.3 17.1 + - - +
143K LYS* 2.9 58.2 + - - +
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Residues in contact with GLU 140 (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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61K GLU* 5.2 8.3 - - - +
65K HIS* 4.9 20.1 + - + +
135K THR 5.5 2.2 - - - +
136K HIS* 3.3 25.3 - - - +
137K TYR* 3.3 8.4 + - - +
138K LEU 3.3 0.2 - - - -
139K ASN* 1.3 79.8 - - - +
141K GLN* 1.3 62.4 + - - +
143K LYS* 3.0 33.0 + - - +
144K ALA* 3.0 29.8 + - - +
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Residues in contact with GLN 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65K HIS* 4.6 6.9 - - - -
107K GLU* 2.8 52.0 + - - +
110K VAL* 3.8 12.3 - - - +
111K ASN* 3.4 25.6 - - + +
114K LEU* 3.4 32.8 - - + +
137K TYR* 3.0 14.6 + - - +
138K LEU 3.7 4.3 - - - +
139K ASN 3.2 0.2 - - - -
140K GLU* 1.3 76.1 - - - +
142K VAL* 1.3 66.7 + - - +
144K ALA* 3.2 3.4 + - - +
145K ILE* 2.9 31.2 + - + +
201K FE 3.9 13.9 - - - -
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Residues in contact with VAL 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K ASN* 5.0 11.2 - - - +
138K LEU* 3.1 20.0 + - + +
139K ASN* 3.3 17.7 + - - +
141K GLN* 1.3 76.3 - - - +
143K LYS* 1.4 58.6 + - + +
145K ILE* 3.4 8.4 + - + +
146K LYS* 3.0 30.3 + - + +
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Residues in contact with LYS 143 (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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139K ASN* 2.9 44.1 + - - +
140K GLU* 3.0 37.5 + - - +
142K VAL* 1.4 76.9 - - + +
144K ALA* 1.3 57.5 + - - +
146K LYS* 3.4 6.1 + - - +
147K GLU* 2.9 31.2 + - - +
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Residues in contact with ALA 144 (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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107K GLU* 3.9 28.5 - - + +
140K GLU 3.0 18.6 + - - +
141K GLN* 3.2 4.2 + - - +
143K LYS* 1.3 76.2 - - - +
145K ILE* 1.3 56.8 + - - +
147K GLU* 3.8 6.5 - - - +
148K LEU* 2.9 39.2 + - + +
202K MG 4.4 14.6 - - - -
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Residues in contact with ILE 145 (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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104K LEU* 3.7 22.2 - - + +
107K GLU* 3.8 34.3 - - + +
108K LYS* 4.0 24.7 - - + -
111K ASN* 3.9 26.7 - - + +
141K GLN 2.9 22.7 + - - +
142K VAL* 3.8 6.7 - - + +
144K ALA* 1.3 76.5 - - - +
146K LYS* 1.3 58.9 + - - +
148K LEU* 3.5 2.4 + - - -
149K GLY* 2.9 26.2 + - - -
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Residues in contact with LYS 146 (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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42I ASP* 2.9 37.8 + - - -
43I ARG* 4.9 0.2 - - - +
44I ASP* 3.8 20.2 - - + +
142K VAL* 3.0 21.7 + - + +
143K LYS* 3.7 6.3 - - - +
145K ILE* 1.3 77.8 - - - +
147K GLU* 1.3 56.9 + - - +
149K GLY* 3.4 1.7 + - - -
150K ASP* 2.8 66.4 + - - +
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Residues in contact with GLU 147 (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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49I LYS* 5.3 9.6 + - - +
54K TYR* 2.6 32.7 + - - +
58K GLN* 4.1 6.8 + - - -
143K LYS 2.9 18.3 + - - +
144K ALA* 3.8 5.8 - - - +
146K LYS* 1.3 77.7 - - - +
148K LEU* 1.3 58.2 + - - +
150K ASP* 3.2 12.2 + - - +
151K HIS* 3.0 50.5 + - + +
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Residues in contact with LEU 148 (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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34K TYR* 3.8 9.2 - - - +
54K TYR* 3.7 25.8 - - + +
55K PHE* 5.1 0.2 - - + -
100K MET* 3.8 25.7 - - - +
103K ALA* 3.7 28.3 - - + +
104K LEU* 3.8 17.5 - - + +
107K GLU* 3.6 30.3 - - + -
144K ALA* 2.9 24.3 + - + +
145K ILE* 3.9 2.9 - - - +
147K GLU* 1.3 74.7 - - - +
149K GLY* 1.3 57.6 + - - +
151K HIS* 3.3 5.5 + - + +
152K VAL* 2.9 34.8 + - - +
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Residues in contact with GLY 149 (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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44I ASP* 4.0 15.9 - - - +
104K LEU* 4.2 16.4 - - - +
145K ILE 2.9 14.9 + - - -
146K LYS 3.7 3.1 - - - -
148K LEU* 1.3 73.6 - - - +
150K ASP* 1.3 65.2 + - - +
152K VAL* 3.3 4.1 + - - +
153K THR* 2.9 27.9 + - - -
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Residues in contact with ASP 150 (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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43I ARG 4.0 0.3 - - - +
44I ASP* 3.2 18.8 - - - -
47I ALA* 3.8 21.3 - - + +
49I LYS* 4.5 20.6 + - - +
146K LYS* 2.8 51.6 + - - +
147K GLU* 3.2 11.2 + - - +
149K GLY* 1.3 76.1 - - - +
151K HIS* 1.3 61.9 + - + +
153K THR* 3.3 2.1 + - - -
154K ASN* 3.0 38.0 + - - +
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Residues in contact with HIS 151 (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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49I LYS* 5.4 7.6 - - - -
54K TYR* 3.8 21.2 + + - -
100K MET* 3.8 33.2 - - + -
147K GLU* 3.0 40.9 + - + +
148K LEU* 3.6 6.7 - - - +
150K ASP* 1.3 77.8 - - + +
152K VAL* 1.3 66.5 + - - +
154K ASN* 3.3 2.2 + - - +
155K LEU* 2.9 30.2 + - - +
170K PHE* 3.6 22.9 - + + -
174K THR* 3.6 25.8 - - + +
175K LEU* 3.9 11.6 - - + +
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Residues in contact with VAL 152 (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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97K LEU* 3.7 14.4 - - + +
100K MET* 3.7 35.7 - - + +
101K GLU* 3.7 11.7 - - + +
104K LEU* 4.5 12.1 - - + -
148K LEU 2.9 21.9 + - - +
149K GLY* 3.7 6.5 - - - +
151K HIS* 1.3 75.7 - - - +
153K THR* 1.3 57.7 + - - +
155K LEU 3.3 0.2 + - - -
156K ARG* 2.9 71.1 + - - +
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Residues in contact with THR 153 (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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44I ASP* 2.6 25.7 + - - +
45I ASP* 3.6 34.9 - - - +
46I VAL 3.8 15.0 - - - +
47I ALA* 4.2 1.1 - - + -
149K GLY 2.9 12.3 + - - -
150K ASP 3.6 3.8 - - - -
152K VAL* 1.3 77.4 - - - +
154K ASN* 1.3 58.2 + - - +
156K ARG* 3.3 12.3 + - - +
157K LYS* 2.9 41.2 + - + +
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Residues in contact with ASN 154 (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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46I VAL 4.4 3.0 - - - +
47I ALA* 2.8 36.6 + - - +
48I LEU* 3.9 10.6 - - - +
168I TYR* 3.5 26.7 - - + +
172I LYS* 4.9 1.1 + - - -
150K ASP* 3.0 28.7 + - - +
151K HIS* 3.9 3.9 + - - +
153K THR* 1.3 76.2 - - - +
155K LEU* 1.3 58.6 + - - +
157K LYS* 3.3 6.9 + - - +
158K MET* 2.8 38.1 + - - +
170K PHE* 3.9 20.1 - - + -
174K THR* 5.7 0.2 - - - -
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Residues in contact with LEU 155 (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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51K PHE* 4.1 7.0 - - + -
97K LEU* 3.9 31.2 - - + +
100K MET* 4.0 20.4 - - + -
151K HIS 2.9 21.5 + - - +
152K VAL 3.8 3.1 - - - +
154K ASN* 1.3 76.8 - - - +
156K ARG* 1.3 63.5 + - - +
158K MET* 3.4 8.3 + - - +
159K GLY 3.4 0.2 + - - -
160K ALA* 3.0 32.3 + - + +
166K ALA 4.5 2.2 - - - +
167K GLU* 4.1 29.4 - - + +
170K PHE* 3.7 43.5 - - + -
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Residues in contact with ARG 156 (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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97K LEU* 3.9 17.5 - - + +
101K GLU* 2.7 30.8 + - - +
104K LEU* 6.3 0.2 - - - +
152K VAL* 2.9 39.7 + - - +
153K THR* 3.7 10.1 + - - +
155K LEU* 1.3 78.9 - - - +
157K LYS* 1.3 63.6 + - + +
159K GLY* 3.1 15.4 + - - -
160K ALA 4.2 8.4 + - - +
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Residues in contact with LYS 157 (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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45I ASP 3.5 25.4 + - - -
46I VAL* 4.5 11.7 - - - +
48I LEU* 6.4 1.8 - - + -
164I GLY* 3.3 38.0 + - - +
165I LEU 3.5 1.2 + - - -
153K THR* 2.9 30.0 + - + +
154K ASN* 3.7 7.2 - - - +
156K ARG* 1.3 78.0 - - + +
158K MET* 1.3 59.9 + - + +
159K GLY 3.5 0.7 + - - -
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Residues in contact with MET 158 (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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165I LEU* 3.9 42.1 - - + +
168I TYR* 3.5 61.0 - - + -
154K ASN 2.8 22.8 + - - +
155K LEU* 3.7 4.3 - - - +
156K ARG 3.2 0.2 - - - -
157K LYS* 1.3 77.0 - - + +
159K GLY* 1.3 55.9 + - - +
160K ALA 3.7 0.2 - - - -
163K SER* 4.4 3.6 - - - -
166K ALA* 3.2 45.6 - - + +
169K LEU* 3.9 5.2 - - + -
170K PHE* 3.6 24.2 - - - +
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Residues in contact with GLY 159 (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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156K ARG 3.1 11.7 + - - -
157K LYS 3.3 1.8 + - - -
158K MET* 1.3 77.2 - - - +
160K ALA* 1.3 65.8 + - - +
162K GLU* 3.4 9.0 + - - +
163K SER* 2.9 30.2 + - - -
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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