Contacts of the helix formed by residues 138 - 149 (chain F) in PDB entry 5L08
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 ASN 138 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17F GLU* 2.9 35.2 + - - +
20F ALA* 5.7 5.2 - - + +
109F SER* 4.9 3.1 - - - -
117F LEU* 5.8 2.7 - - - -
136F ASP 3.1 7.7 + - - +
137F MET* 1.3 74.1 - - - +
139F LEU* 1.3 75.2 + - - +
140F LEU* 2.9 26.4 + - + +
141F ASP* 2.8 41.2 + - - +
142F ILE* 2.8 13.4 + - - +
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ILE* 4.0 11.7 - - + -
109F SER* 3.8 28.9 - - - -
112F VAL* 4.1 9.2 - - + -
117F LEU* 3.7 37.4 - - + +
120F PHE* 3.7 39.7 - - + -
137F MET 3.7 2.2 + - - -
138F ASN* 1.3 78.2 + - - +
140F LEU* 1.3 58.0 + - - +
142F ILE* 3.2 11.1 + - + +
143F PHE* 2.9 53.8 + - + -
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Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F GLU* 5.5 1.8 - - - +
20F ALA* 4.7 2.2 - - + +
21F SER* 4.0 27.6 - - - +
24F PHE* 3.6 51.9 - - + -
105F LEU 3.9 6.3 - - - +
106F TYR* 4.1 7.9 - - + -
109F SER* 3.8 30.1 - - - +
138F ASN* 2.9 19.9 + - - +
139F LEU* 1.3 74.2 - - - +
141F ASP* 1.3 63.5 + - - +
143F PHE* 3.3 17.7 + - + +
144F ILE* 3.1 30.2 + - - +
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Residues in contact with ASP 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ALA* 5.9 2.6 - - - +
136F ASP 4.5 4.5 - - - +
137F MET* 3.9 15.3 - - + +
138F ASN* 2.8 34.0 + - - +
140F LEU* 1.3 78.1 - - - +
142F ILE* 1.3 64.2 + - - +
144F ILE* 3.2 21.9 + - + +
145F GLU* 3.1 24.6 + - - +
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Residues in contact with ILE 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F LEU* 5.6 1.3 - - + -
120F PHE* 3.9 36.3 - - + -
121F LYS* 3.9 30.5 - - + -
124F LEU* 4.2 17.5 - - + -
131F CYS* 5.0 4.9 - - - -
133F LEU* 5.7 0.9 - - + -
137F MET* 3.8 23.3 - - + +
138F ASN 2.8 15.6 + - - +
139F LEU* 3.3 18.4 - - + +
141F ASP* 1.3 74.1 - - - +
143F PHE* 1.3 59.3 + - + +
145F GLU* 3.0 6.5 + - + +
146F MET* 2.8 43.8 + - + +
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Residues in contact with PHE 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F PHE* 3.7 9.6 - + + -
105F LEU* 3.5 45.3 - - + -
108F ILE* 4.2 11.0 - - + -
120F PHE* 5.0 0.7 - + - -
139F LEU* 2.9 52.1 + - + -
140F LEU* 3.3 25.6 - - + +
141F ASP 3.3 0.2 - - - -
142F ILE* 1.3 75.4 - - - +
144F ILE* 1.3 58.1 + - - +
146F MET* 3.2 17.0 + - - -
147F GLU* 2.8 28.1 + - - +
152F LEU* 3.3 25.9 - - + +
160F LEU* 3.8 27.4 - - + -
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Residues in contact with ILE 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F PHE* 4.4 6.1 - - + -
27F LEU* 3.8 33.0 - - + -
32F GLN* 3.4 37.2 - - - +
35F GLN* 5.4 4.0 - - - +
140F LEU 3.1 17.2 + - - +
141F ASP* 3.3 24.9 - - - +
142F ILE 3.2 0.2 - - - -
143F PHE* 1.3 75.9 - - - +
145F GLU* 1.3 59.4 + - - +
147F GLU* 3.1 13.3 + - + +
148F LYS* 3.0 38.6 + - - +
15H ASP* 5.8 0.2 - - - +
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Residues in contact with GLU 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F CYS* 4.6 13.2 - - - -
132F LYS* 5.3 7.8 + - - +
137F MET* 3.9 19.4 - - + +
141F ASP 3.1 15.5 + - - +
142F ILE* 3.0 10.0 + - - +
144F ILE* 1.3 77.1 - - - +
146F MET* 1.3 61.7 + - + +
148F LYS* 2.9 36.2 + - - +
149F ARG* 2.8 63.0 + - - +
15H ASP* 4.9 0.3 - - - +
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Residues in contact with MET 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F PHE* 4.9 5.4 - - + -
124F LEU* 5.5 7.2 - - + -
142F ILE* 2.8 28.0 + - + +
143F PHE* 3.2 35.9 + - - +
145F GLU* 1.3 75.0 - - + +
147F GLU* 1.3 62.6 + - - +
149F ARG* 3.3 1.4 + - - +
150F VAL 3.1 3.6 + - - -
151F ILE* 2.8 73.0 + - + +
152F LEU* 3.5 15.3 - - + -
159F ILE* 4.2 14.8 - - + -
160F LEU* 3.9 22.9 - - + -
163F VAL* 6.4 0.4 - - + -
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Residues in contact with GLU 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F PHE* 4.2 4.0 - - - -
27F LEU* 4.3 4.2 - - - +
32F GLN* 5.7 2.7 - - - +
101F TYR* 4.9 5.2 - - - +
102F ARG* 2.7 45.5 + - - -
143F PHE 2.8 21.6 + - - +
144F ILE* 3.3 17.3 + - + +
146F MET* 1.3 72.8 - - - +
148F LYS* 1.3 65.5 + - - +
150F VAL* 2.9 12.9 + - - +
152F LEU* 4.1 28.2 - - + +
73H ASP* 3.3 20.3 - - + +
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Residues in contact with LYS 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F GLN* 4.6 5.2 - - - +
144F ILE* 3.0 28.9 + - + +
145F GLU* 2.9 45.7 + - - +
147F GLU* 1.3 76.3 - - + +
149F ARG* 1.3 59.3 + - - +
15H ASP* 3.0 28.0 + - - -
18H ASP* 3.0 27.3 + - - +
69H ILE 5.4 1.6 - - - +
70H ASN* 3.0 14.6 - - + +
71H ARG* 3.5 30.1 - - - +
72H LEU 2.9 28.2 + - - -
73H ASP* 3.1 17.2 + - - +
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Residues in contact with ARG 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F ILE* 6.4 0.7 - - - -
130F LYS* 2.9 54.8 + - + +
131F CYS* 3.6 15.8 - - - +
132F LYS* 3.8 8.1 - - - +
145F GLU* 2.8 63.8 + - - +
146F MET 3.3 3.5 + - - +
147F GLU 3.1 0.6 - - - -
148F LYS* 1.3 82.6 - - - +
150F VAL* 1.3 72.1 + - - +
151F ILE* 3.2 28.8 + - + +
70H ASN* 3.9 33.9 - - + +
72H LEU* 3.7 21.2 - - + +
83H LYS* 5.5 1.4 - - - +
110H GLU* 5.1 2.2 + - - -
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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