Contacts of the helix formed by residues 138 - 160 (chain C) in PDB entry 5OMA
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 ASP 138 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C GLY* 1.3 74.2 - - - -
139C ASP* 1.3 60.8 + - - +
141C LYS* 3.7 20.7 + - - +
142C ARG* 3.3 33.2 + - - +
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Residues in contact with ASP 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ALA* 5.1 4.7 - - + -
137C GLY* 4.7 3.6 - - - +
138C ASP* 1.3 78.4 + - - +
140C LYS* 1.4 62.0 + - - +
141C LYS 3.2 4.1 + - - -
142C ARG* 3.0 35.8 + - - +
143C ILE* 3.2 47.2 + - + +
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Residues in contact with LYS 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ALA* 4.8 10.0 + - + +
135C ALA* 3.4 31.3 + - + +
136C THR* 3.5 22.4 - - + +
137C GLY 3.2 17.1 + - - +
139C ASP* 1.4 75.2 - - - +
141C LYS* 1.3 76.9 + - - +
143C ILE* 4.2 2.3 - - - +
144C ILE* 3.0 53.7 + - + +
183C ILE* 3.8 17.5 + - - +
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Residues in contact with LYS 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C THR 4.7 2.5 - - - -
137C GLY 3.9 14.4 - - - +
138C ASP* 3.9 12.8 - - - +
139C ASP 3.2 0.4 - - - -
140C LYS* 1.3 119.2 - - - +
142C ARG* 1.4 65.1 + - + +
144C ILE* 3.4 12.2 + - - +
145C ASP* 3.1 27.0 + - - +
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Residues in contact with ARG 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ASP* 3.3 33.4 + - - +
139C ASP* 3.0 40.4 + - - +
141C LYS* 1.4 75.4 - - + +
143C ILE* 1.3 59.4 + - + +
145C ASP* 3.1 8.8 + - - +
146C SER* 2.9 32.1 + - - +
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Residues in contact with ILE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C TYR* 3.2 39.1 - - + +
131C LEU* 3.9 18.8 - - + +
132C ALA* 3.8 15.0 - - + +
135C ALA* 3.8 23.8 - - + -
139C ASP* 3.2 38.9 + - - +
140C LYS* 4.2 3.6 - - - +
142C ARG* 1.3 73.3 - - + +
144C ILE* 1.4 64.9 + - - +
146C SER* 3.1 9.1 + - - -
147C ALA* 3.0 22.4 + - - +
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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
----------------------------------------------------------
132C ALA* 4.3 8.3 - - + -
140C LYS* 3.0 58.5 + - + +
141C LYS* 3.4 12.3 + - + +
143C ILE* 1.4 74.4 - - - +
145C ASP* 1.3 63.8 + - - +
147C ALA* 3.3 4.0 + - - +
148C ARG* 2.9 27.2 + - - +
179C PHE* 3.3 29.4 - - + -
183C ILE* 3.6 28.5 - - + +
184C ALA* 4.6 12.1 - - + -
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Residues in contact with ASP 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LYS 3.1 13.9 + - - +
142C ARG* 3.1 11.4 + - - +
144C ILE* 1.3 79.9 - - - +
146C SER* 1.3 58.0 + - - +
148C ARG* 3.5 20.9 + - - +
149C SER* 2.9 33.5 + - - -
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Residues in contact with SER 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C TYR* 3.6 39.4 + - - -
142C ARG* 2.9 16.5 + - - +
143C ILE* 3.1 7.9 + - - -
145C ASP* 1.3 75.1 - - - +
147C ALA* 1.4 59.8 + - - +
149C SER* 3.7 7.7 + - - -
150C ALA* 3.2 23.0 + - - +
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Residues in contact with ALA 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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125C GLY* 3.8 13.6 - - - +
128C TYR* 3.6 24.3 - - + +
129C ARG* 3.9 8.3 - - - +
132C ALA* 6.3 0.4 - - + -
143C ILE 3.0 8.4 + - - +
144C ILE* 3.4 10.3 - - - +
146C SER* 1.4 74.6 - - - +
148C ARG* 1.4 58.2 + - - +
150C ALA* 3.4 6.0 - - - +
151C TYR* 3.0 35.8 + - + -
179C PHE* 3.9 17.9 - - + -
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Residues in contact with ARG 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ILE* 2.9 20.1 + - - +
145C ASP* 3.3 25.1 + - - +
147C ALA* 1.4 71.6 - - - +
149C SER* 1.4 57.0 + - - +
150C ALA 3.1 4.3 - - - -
151C TYR* 3.1 4.3 + - - +
152C GLN* 3.0 32.0 + - + +
176C PHE* 4.1 10.4 - - + -
179C PHE* 3.7 22.2 - - + -
180C HIS* 3.5 24.0 + - - -
184C ALA* 3.3 31.3 - - - +
186C SER* 4.3 5.7 + - - -
189C GLU* 4.2 11.1 + - - -
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Residues in contact with SER 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ASP* 2.9 21.8 + - - -
146C SER* 3.7 9.5 + - - -
148C ARG* 1.4 73.0 - - - +
150C ALA* 1.4 58.5 + - - +
152C GLN* 4.2 6.8 - - - +
153C GLU* 3.6 23.0 + - - +
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Residues in contact with ALA 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 3.3 35.6 - - + +
124C LYS* 4.5 12.3 - - + -
125C GLY* 4.0 19.7 - - - +
128C TYR* 5.1 0.4 - - + -
146C SER 3.2 18.1 + - - +
147C ALA 3.4 6.5 - - - +
148C ARG 3.1 0.2 - - - -
149C SER* 1.4 78.2 + - - +
151C TYR* 1.4 62.0 + - - +
153C GLU* 3.8 0.4 + - - -
154C ALA* 3.3 12.8 + - - +
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Residues in contact with TYR 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LYS* 4.0 18.2 - - + -
125C GLY* 3.6 21.5 - - - -
126C ASP* 2.7 26.2 + - - -
129C ARG* 3.0 19.9 + - - -
147C ALA 3.0 24.6 + - - +
148C ARG 3.1 0.6 + - - +
150C ALA* 1.4 74.6 - - - +
152C GLN* 1.4 53.5 + - - +
154C ALA* 3.5 3.7 + - - +
155C MET* 2.8 37.4 + - - +
172C LEU* 3.7 24.6 - - + +
175C ASN* 3.8 12.1 - - + +
176C PHE* 3.3 46.7 - + + -
179C PHE* 3.8 25.6 - + + -
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Residues in contact with GLN 152 (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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148C ARG* 3.0 18.5 + - + +
149C SER* 4.5 6.7 - - - +
150C ALA 3.4 0.2 - - - -
151C TYR* 1.4 73.9 - - - +
153C GLU* 1.4 61.7 - - - +
154C ALA 3.2 0.4 - - - -
155C MET* 3.2 16.5 + - - +
156C ASP* 3.2 37.3 + - - +
176C PHE* 3.4 25.7 - - - -
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Residues in contact with GLU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 3.4 33.1 - - + +
149C SER 3.6 17.7 + - - +
150C ALA* 4.1 4.7 - - - +
151C TYR 3.5 0.4 - - - -
152C GLN* 1.4 76.0 - - - +
154C ALA* 1.3 57.8 + - - +
156C ASP* 3.8 5.4 + - - +
157C ILE* 3.3 44.7 + - + +
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Residues in contact with ALA 154 (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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118C VAL* 4.3 10.4 - - + +
121C LEU* 3.8 30.9 - - + +
122C LYS 4.5 0.7 - - - +
150C ALA 3.3 16.6 + - - +
151C TYR* 3.5 6.1 - - - +
152C GLN 3.2 0.2 - - - -
153C GLU* 1.3 76.7 - - - +
155C MET* 1.4 57.6 + - - +
156C ASP 3.2 6.0 + - - -
157C ILE* 3.6 6.9 + - - -
158C SER* 3.4 12.0 + - - -
172C LEU* 3.3 30.6 - - + +
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Residues in contact with MET 155 (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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151C TYR 2.8 23.6 + - - +
152C GLN* 3.2 14.0 + - - +
154C ALA* 1.4 74.1 - - - +
156C ASP* 1.4 60.2 + - - +
158C SER* 3.1 19.7 + - - -
159C LYS* 3.0 50.9 + - + +
169C ARG* 5.3 1.8 - - - +
172C LEU* 4.1 14.6 - - + -
173C ALA* 4.2 27.4 - - + -
176C PHE* 3.5 22.9 - - + -
193C LEU* 3.9 26.0 - - + -
197C THR* 5.6 0.4 - - - +
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Residues in contact with ASP 156 (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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152C GLN* 3.2 32.6 + - - +
153C GLU* 4.3 6.3 - - - +
154C ALA 3.2 0.8 - - - -
155C MET* 1.4 77.9 - - - +
157C ILE* 1.4 58.7 + - + +
158C SER 3.1 7.2 + - - -
159C LYS* 3.0 24.4 + - - +
160C LYS* 3.4 39.4 + - + +
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Residues in contact with ILE 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ALA* 4.3 16.5 - - + +
117C ARG* 5.3 16.6 - - + -
118C VAL* 3.4 23.2 - - + +
121C LEU* 4.2 12.6 - - + -
153C GLU* 3.3 40.3 + - + +
154C ALA* 3.6 3.6 + - - +
156C ASP* 1.4 75.4 - - + +
158C SER* 1.4 54.4 + - - +
160C LYS* 5.4 0.4 - - - -
161C GLU* 3.3 34.9 - - + +
162C MET* 4.5 0.9 - - - +
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Residues in contact with SER 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL* 4.5 3.6 - - - -
154C ALA 3.4 14.5 + - - -
155C MET* 3.1 20.8 + - - -
156C ASP 3.1 0.8 - - - -
157C ILE* 1.4 77.1 - - - +
159C LYS* 1.4 71.6 + - - +
160C LYS 3.3 0.9 - - - -
161C GLU 3.8 0.9 - - - -
162C MET* 2.8 47.0 + - - +
169C ARG* 3.4 28.7 - - - +
172C LEU* 4.1 10.4 - - - +
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Residues in contact with LYS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C MET* 3.0 42.3 + - + +
156C ASP* 3.0 28.1 + - - -
158C SER* 1.4 83.4 + - - +
160C LYS* 1.3 86.3 + - - +
161C GLU 3.7 0.3 + - - -
162C MET 3.9 8.1 + - - +
169C ARG* 3.9 29.6 + - - +
200C GLU* 5.9 1.6 - - - +
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Residues in contact with LYS 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ASP* 3.4 31.1 + - + +
157C ILE* 5.4 0.2 - - - -
158C SER 3.3 0.4 - - - -
159C LYS* 1.3 120.8 - - - +
161C GLU* 1.3 66.4 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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