Contacts of the helix formed by residues 139 - 156 (chain g) in PDB entry 5KZ5
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 139 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101g SER* 4.2 5.9 + - - -
122g ASN* 4.0 7.9 - - - -
125g ILE* 3.3 11.8 - - - +
126g ALA* 3.5 19.1 + - - -
129g LEU* 3.3 20.3 - - - +
131g LEU* 3.1 25.0 - - - +
136g LEU 3.2 8.5 + - - -
138g CYS* 1.4 77.9 - - - +
140g MET* 1.4 54.3 + - - +
142g ALA* 3.2 11.2 + - - +
143g GLU* 3.0 23.7 + - - +
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Residues in contact with MET 140 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H SER 5.0 2.7 - - - +
90H LEU* 3.7 22.7 - - + +
138L GLY* 4.1 19.3 - - - +
139L ASP* 3.2 26.9 - - - +
66g ALA* 5.5 2.4 - - + +
67g PRO 4.7 4.7 - - - +
68g ALA* 3.8 25.1 - - + -
122g ASN* 3.9 13.2 - - + +
136g LEU* 3.0 25.2 + - + +
137g HIS* 4.0 17.9 - - + +
138g CYS 3.3 0.2 - - - -
139g SER* 1.4 74.4 - - - +
141g LEU* 1.4 59.1 + - - +
143g GLU* 3.4 23.6 - - - +
144g ASP* 3.4 8.7 + - - +
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Residues in contact with LEU 141 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G ARG* 3.7 7.9 - - - +
383M SER* 3.8 11.4 - - - +
64g VAL* 3.8 14.4 - - + +
66g ALA* 3.3 32.8 - - - +
68g ALA* 3.9 10.7 - - + +
69g CYS 3.3 27.6 - - - +
70g GLY 3.2 15.5 - - - +
71g ASP* 3.2 34.3 - - + +
137g HIS 3.9 1.4 + - - -
138g CYS 3.2 6.8 + - - +
140g MET* 1.4 76.7 - - - +
142g ALA* 1.3 61.0 + - - +
144g ASP* 3.3 7.4 + - + +
145g ALA* 3.2 17.8 + - - +
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Residues in contact with ALA 142 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71g ASP* 3.5 6.0 + - - +
73g MET* 3.9 27.1 - - + +
101g SER* 4.1 23.3 - - - +
102g SER* 5.4 0.2 - - - -
105g ALA* 5.0 3.1 - - + -
125g ILE* 4.2 9.4 - - + -
138g CYS 3.3 5.7 + - - +
139g SER* 3.2 14.3 + - - +
141g LEU* 1.3 74.6 - - - +
143g GLU* 1.4 61.7 + - - +
145g ALA* 3.3 5.2 + - - +
146g ILE* 3.2 26.5 + - + +
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Residues in contact with GLU 143 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H SER 3.7 10.9 - - - +
90H LEU* 4.4 0.3 - - - -
92H GLU* 3.1 24.8 - - - +
120g ILE* 3.1 31.7 - - + +
122g ASN* 3.1 41.4 + - - +
125g ILE* 3.7 14.5 - - + +
139g SER 3.0 12.0 + - - +
140g MET* 3.4 18.4 - - - +
142g ALA* 1.4 73.9 - - - +
144g ASP* 1.3 55.7 + - - +
146g ILE* 3.2 6.8 + - - +
147g LYS* 2.9 43.1 + - + +
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Residues in contact with ASP 144 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H HIS* 4.7 9.2 + - - -
88H GLY* 4.2 2.9 - - - -
89H SER* 3.2 29.3 + - - +
63g LEU 4.6 1.4 - - - +
64g VAL* 4.0 2.6 - - - -
65g GLY* 3.2 28.9 + - - -
66g ALA* 3.3 23.9 + - + -
140g MET 3.4 8.4 + - - +
141g LEU* 3.3 11.8 + - + +
143g GLU* 1.3 76.1 - - - +
145g ALA* 1.4 59.3 + - - +
147g LYS* 3.3 13.6 + - - +
148g ALA* 3.0 29.9 + - - +
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Residues in contact with ALA 145 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62g GLY* 4.1 5.1 - - - -
63g LEU 4.9 1.8 - - - +
64g VAL* 3.9 28.7 - - + +
73g MET* 3.8 28.7 - - + -
75g LEU* 4.4 10.0 - - + +
141g LEU 3.2 8.4 + - - +
142g ALA 3.4 9.6 - - - +
143g GLU 3.3 0.2 - - - -
144g ASP* 1.4 76.7 + - - +
146g ILE* 1.4 61.0 + - - +
148g ALA* 3.5 7.5 + - - +
149g ALA* 3.2 21.0 + - - +
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Residues in contact with ILE 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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73g MET* 5.3 0.9 - - + -
75g LEU* 3.7 34.3 - - + -
77g ILE* 4.9 4.3 - - + -
105g ALA* 3.7 37.0 - - + +
106g THR* 4.6 2.2 - - + +
109g VAL* 5.0 13.2 - - + -
117g ALA* 4.9 0.9 - - + +
120g ILE* 3.6 31.0 - - + -
142g ALA 3.2 13.0 + - - +
143g GLU* 3.2 8.4 + - - +
145g ALA* 1.4 72.0 - - - +
147g LYS* 1.3 63.4 + - - +
149g ALA* 3.2 4.7 + - - +
150g LEU* 3.0 41.8 + - + +
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Residues in contact with LYS 147 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H HIS 5.1 2.2 - - - +
87H PRO 5.0 3.3 - - - +
88H GLY* 3.2 34.5 + - - +
89H SER 2.9 28.0 + - - +
90H LEU 3.4 0.4 + - - -
92H GLU* 3.0 25.9 + - - -
120g ILE* 4.5 6.7 - - + -
143g GLU* 2.9 42.8 + - + +
144g ASP* 3.4 12.3 - - - +
146g ILE* 1.3 75.1 - - - +
148g ALA* 1.3 53.0 + - - +
150g LEU* 3.4 9.5 + - - +
151g ALA* 2.8 35.3 + - - +
167g LYS* 3.7 28.8 - - + +
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Residues in contact with ALA 148 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G SER* 4.6 4.7 - - - +
85H GLY 3.5 21.0 - - - +
86H HIS* 4.3 5.8 - - + +
62g GLY* 3.7 3.4 - - - -
63g LEU 3.3 33.7 - - - +
144g ASP* 3.0 16.6 + - - +
145g ALA 3.6 5.4 - - - +
147g LYS* 1.3 75.6 - - - +
149g ALA* 1.4 58.8 + - - +
151g ALA* 4.2 0.2 - - - -
152g ASP* 3.1 28.2 + - - +
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Residues in contact with ALA 149 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60g GLY* 3.8 5.9 - - - -
61g THR 4.2 2.9 - - - +
62g GLY* 3.4 25.5 - - - +
75g LEU* 3.6 33.7 - - + +
77g ILE* 3.7 14.5 - - + +
145g ALA 3.2 3.7 + - - +
146g ILE 3.2 5.2 + - - +
148g ALA* 1.4 78.6 - - - +
150g LEU* 1.4 55.6 + - - +
152g ASP* 3.6 2.8 + - - +
153g TYR* 3.1 27.4 + - - +
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Residues in contact with LEU 150 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77g ILE* 3.5 21.5 - - + -
79g VAL* 4.2 19.7 - - + -
85g ILE* 4.8 0.9 - - + -
114g VAL* 5.3 3.6 - - + -
117g ALA* 3.3 48.2 - - + +
118g LEU* 3.7 26.1 - - + +
120g ILE* 4.9 1.8 - - + -
146g ILE* 3.0 34.5 + - + +
147g LYS* 3.8 7.4 - - - +
149g ALA* 1.4 72.0 - - - +
151g ALA* 1.4 60.4 + - - +
153g TYR* 3.8 6.7 - - + +
154g LYS* 2.9 29.8 + - - +
157g GLN* 4.8 2.2 + - - +
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Residues in contact with ALA 151 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H GLY* 3.4 21.3 - - - +
86H HIS 3.4 27.4 - - - +
87H PRO* 5.5 0.4 - - + +
118g LEU* 5.1 1.1 - - - +
147g LYS 2.8 18.8 + - - +
148g ALA 3.7 0.4 - - - +
150g LEU* 1.4 73.9 - - - +
152g ASP* 1.3 62.7 + - - +
154g LYS* 3.3 0.6 + - - -
155g LEU* 3.1 11.6 + - - +
163g GLU* 2.9 33.0 - - - +
167g LYS* 5.6 3.1 - - - +
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Residues in contact with ASP 152 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G GLY 3.0 33.1 - - - +
62G LEU* 3.6 22.0 - - + +
64G GLN* 3.4 15.6 + - - -
74H TYR* 5.0 1.2 + - - -
85H GLY* 4.5 2.9 + - - +
60g GLY* 3.9 2.9 - - - -
61g THR 3.4 20.5 + - - +
148g ALA 3.1 16.0 + - - +
149g ALA 3.6 5.8 - - - +
151g ALA* 1.3 77.3 - - - +
153g TYR* 1.4 62.9 + - - +
155g LEU* 3.4 22.2 - - - +
156g LYS* 3.7 15.6 + - - +
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Residues in contact with TYR 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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57g LYS* 3.5 24.7 + - + +
58g ASN 3.2 27.1 - - - -
60g GLY* 4.2 14.6 - - - -
77g ILE* 5.8 0.2 - - + -
79g VAL* 3.0 53.7 + - + -
80g ASP 4.1 2.7 - - - -
81g GLU* 2.9 33.7 + - + +
149g ALA 3.1 17.7 + - - +
150g LEU* 3.8 8.5 - - + +
151g ALA 3.3 0.2 - - - -
152g ASP* 1.4 77.6 + - - +
154g LYS* 1.4 54.4 + - - +
155g LEU 3.2 0.7 - - - -
156g LYS* 3.0 14.8 + - + +
157g GLN* 3.0 53.7 + - + -
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Residues in contact with LYS 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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115g GLU* 4.4 7.1 + - - -
118g LEU* 3.8 32.5 - - + +
150g LEU 2.9 18.4 + - - +
151g ALA 3.3 0.6 + - - +
153g TYR* 1.4 70.7 - - - +
155g LEU* 1.4 58.3 + - - +
156g LYS 3.3 0.4 - - - -
157g GLN* 2.9 43.5 - - + +
159g PRO* 3.6 34.2 - - + +
161g LYS 4.4 2.0 + - - -
162g GLY* 3.5 22.7 - - - -
163g GLU* 3.6 37.1 - - + +
167g LYS 3.6 14.1 + - - +
82h LYS* 4.2 2.4 - - - +
161i LYS* 4.9 4.8 - - - +
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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
----------------------------------------------------------
43G ARG* 6.0 0.4 - - - +
62G LEU* 3.7 35.9 - - + -
74H TYR* 3.6 26.8 - - + +
75H LEU* 3.3 47.0 - - - +
77H ASN* 3.3 28.7 - - + +
84H LEU* 5.4 4.7 - - + -
151g ALA 3.1 11.8 + - - +
152g ASP* 3.4 15.5 - - - +
153g TYR 3.2 0.2 - - - -
154g LYS* 1.4 75.7 - - - +
156g LYS* 1.4 60.8 + - - +
157g GLN 3.6 0.6 - - - +
163g GLU* 3.7 8.3 - - - +
82h LYS* 3.9 13.3 - - + +
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Residues in contact with LYS 156 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G GLY 5.5 0.4 - - - -
64G GLN* 3.4 32.9 - - - +
69G LYS* 3.9 30.5 - - + +
74H TYR* 4.5 17.7 - - + +
75H LEU* 3.3 13.6 - - - +
57g LYS* 3.1 48.9 + - + +
58g ASN* 3.4 17.6 - - - +
59g VAL 3.0 30.1 + - - -
60g GLY 4.5 0.2 - - - +
152g ASP* 3.8 20.3 + - - +
153g TYR* 3.0 17.1 + - + +
155g LEU* 1.4 77.2 - - - +
157g GLN* 1.4 58.6 + - - +
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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
------------------------------------------------------------
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