Contacts of the helix formed by residues 138 - 149 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C GLU* 3.1 29.9 + - - -
20C ALA* 6.0 4.5 - - + +
109C SER* 4.3 5.0 - - - -
117C LEU* 5.1 1.6 - - - -
136C ASP 3.7 2.8 + - - -
137C MET* 1.3 74.7 - - - +
139C LEU* 1.3 75.2 + - - +
140C LEU* 2.9 29.2 + - + +
141C ASP* 2.8 40.0 + - - +
142C ILE* 2.9 13.0 + - - +
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Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE* 4.1 2.2 - - + -
109C SER* 3.9 18.4 - - - +
112C VAL* 3.7 38.8 - - + -
117C LEU* 4.0 25.8 - - + +
120C PHE* 4.8 18.8 - - + -
124C LEU* 5.9 0.7 - - + -
137C MET 3.9 1.2 + - - -
138C ASN* 1.3 78.7 + - - +
140C LEU* 1.3 56.1 + - - +
142C ILE* 3.2 19.1 + - + +
143C PHE* 2.8 65.1 + - + -
146C MET* 5.9 0.2 - - + -
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 6.0 0.7 - - - +
20C ALA 5.1 1.3 - - - +
21C SER* 4.4 13.7 - - - +
24C PHE* 3.6 50.2 - - + -
105C LEU 3.7 17.7 - - - +
106C TYR* 3.9 19.7 - - + -
109C SER* 3.6 26.5 - - - +
138C ASN* 2.9 20.1 + - - +
139C LEU* 1.3 72.3 - - - +
141C ASP* 1.3 67.8 + - - +
143C PHE* 3.3 14.1 + - + +
144C ILE* 3.0 26.4 + - - +
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Residues in contact with ASP 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ALA* 6.0 1.7 - - - +
136C ASP 4.5 2.8 - - - +
137C MET* 4.1 15.2 - - + -
138C ASN* 2.8 37.0 + - - +
140C LEU* 1.3 76.9 - - - +
142C ILE* 1.3 63.0 + - - +
144C ILE* 3.2 19.7 + - - +
145C GLU* 3.1 27.1 + - - +
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Residues in contact with ILE 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C LEU* 3.8 28.9 - - + -
121C LYS* 5.1 6.1 - - + -
124C LEU* 3.5 38.1 - - + -
131C CYS* 4.7 5.2 - - - -
133C LEU* 4.8 4.9 - - + -
134C ASP 5.9 0.4 - - - +
137C MET* 3.8 31.2 - - + +
138C ASN 2.9 16.7 + - - +
139C LEU* 3.2 16.6 + - + +
141C ASP* 1.3 73.6 - - - +
143C PHE* 1.3 67.0 + - - +
145C GLU* 3.0 5.7 + - - +
146C MET* 2.9 38.8 + - + +
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Residues in contact with PHE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PHE* 4.1 9.2 - + + -
105C LEU* 3.4 47.1 - - + -
108C ILE* 3.9 14.6 - - + -
139C LEU* 2.8 51.4 + - + -
140C LEU* 3.3 26.5 - - + +
142C ILE* 1.3 75.6 - - - +
144C ILE* 1.3 61.5 + - - +
146C MET* 3.2 17.6 + - + -
147C GLU* 2.9 29.8 + - - +
152C LEU* 3.4 19.2 - - + +
160C LEU* 3.8 20.0 - - + -
164C CYS* 6.0 2.5 - - - -
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Residues in contact with ILE 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PHE* 4.0 13.5 - - + -
27C LEU* 3.8 33.9 - - + -
32C GLN* 4.5 13.7 - - + +
33C ARG* 3.8 35.7 - - - +
35C GLN* 5.5 3.4 - - - +
140C LEU 3.0 15.9 + - - +
141C ASP* 3.2 22.0 + - - +
143C PHE* 1.3 75.4 - - - +
145C GLU* 1.3 57.8 + - - +
147C GLU* 3.1 14.3 + - + +
148C LYS* 3.0 32.6 + - + +
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Residues in contact with GLU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG* 3.1 27.2 + - - -
131C CYS* 3.9 16.6 - - - -
132C LYS 5.3 1.6 - - - +
137C MET* 3.8 21.5 - - + -
141C ASP 3.1 17.1 + - - +
142C ILE 3.0 8.6 + - - +
144C ILE* 1.3 76.4 - - - +
146C MET* 1.3 61.0 + - - +
148C LYS* 2.9 25.5 + - - +
149C ARG* 2.7 58.7 + - - +
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Residues in contact with MET 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C LEU* 3.8 21.5 - - + -
127C GLU* 6.2 2.2 - - - -
131C CYS* 5.1 8.7 - - + -
139C LEU* 5.9 0.2 - - + -
142C ILE* 2.9 25.8 + - + +
143C PHE* 3.5 39.0 - - + +
145C GLU* 1.3 73.4 - - - +
147C GLU* 1.3 63.9 + - - +
149C ARG* 3.2 4.0 + - - +
150C VAL 3.1 3.5 + - - -
151C ILE* 2.9 60.2 + - + +
152C LEU* 3.7 11.9 - - + -
160C LEU* 3.7 33.2 - - + -
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Residues in contact with GLU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PHE* 4.4 1.2 - - - -
27C LEU* 5.2 1.4 - - - +
32C GLN* 5.7 8.7 + - - +
101C TYR* 4.5 6.5 - - - +
102C ARG* 2.7 46.1 + - - -
105C LEU* 4.2 11.3 - - - +
143C PHE 2.9 22.8 + - - +
144C ILE* 3.1 15.8 + - + +
146C MET* 1.3 76.2 - - - +
148C LYS* 1.3 57.1 - - - +
150C VAL* 2.7 22.7 + - - +
152C LEU* 3.4 30.0 - - + +
153C GLY* 5.3 0.2 - - - -
73F ASP* 3.5 15.2 - - + +
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Residues in contact with LYS 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C GLN* 3.6 20.4 + - - +
33C ARG* 4.0 15.6 - - - +
144C ILE* 3.0 20.8 + - + +
145C GLU* 2.9 46.2 + - - +
147C GLU* 1.3 76.0 - - - +
149C ARG* 1.3 64.1 + - - +
15F ASP* 5.5 1.4 - - - +
18F ASP* 3.7 18.6 + - - -
69F ILE 5.4 1.7 + - - -
70F ASN 3.1 10.3 - - - +
71F ARG* 3.3 33.4 - - - +
72F LEU 2.9 27.9 + - - -
73F ASP* 3.1 17.9 + - - +
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Residues in contact with ARG 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C ILE* 5.9 0.4 - - + -
130C LYS* 2.7 60.9 + - + -
131C CYS* 3.7 12.5 - - - +
132C LYS* 4.1 4.8 - - - +
145C GLU* 2.7 58.4 + - - +
146C MET* 3.7 7.9 - - - +
147C GLU 3.1 0.6 - - - -
148C LYS* 1.3 86.3 - - - +
150C VAL* 1.3 70.0 + - - +
151C ILE* 3.2 24.5 + - + +
69F ILE 5.5 1.4 + - - -
70F ASN* 3.6 29.4 - - + +
72F LEU* 3.8 19.0 - - + +
110F GLU* 5.1 9.1 + - - -
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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