Contacts of the helix formed by residues 152 - 159 (chain C) in PDB entry 3GHG
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 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150C GLY 3.3 1.2 + - - -
151C LYS* 1.3 81.5 - - - +
153C CYS* 1.3 62.8 + - - +
154C GLN* 3.0 6.8 + - - +
155C ASP* 2.4 41.5 + - - +
156C ILE* 3.4 22.2 + - - +
169C ILE* 3.8 20.3 - - - +
192C THR* 4.6 4.0 - - - +
236C ILE* 5.5 4.0 - - + -
242C ILE* 5.4 4.9 - - - +
244C TYR* 3.4 29.0 + - + +
388C PRO* 3.6 21.6 - - - +
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Residues in contact with CYS 153 (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 ASP* 1.3 73.7 - - - +
154C GLN* 1.3 67.6 + - - +
156C ILE* 3.2 6.6 + - - +
157C ALA* 3.0 15.8 + - - +
169C ILE* 5.0 0.2 - - - +
180C VAL* 3.9 11.0 - - - -
181C TYR 3.9 2.0 - - - -
182C CYS* 2.0 62.9 - - + +
184C ILE* 4.9 0.9 - - - +
190C GLY* 3.4 21.2 - - - +
192C THR* 2.8 36.5 + - - +
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Residues in contact with GLN 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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152C ASP* 3.0 8.2 + - - +
153C CYS* 1.3 77.7 - - - +
155C ASP* 1.3 51.5 + - - +
157C ALA* 2.7 24.1 + - - +
158C ASN* 2.7 46.9 + - - +
188C GLY 2.8 24.4 + - - -
189C ASN* 3.5 5.9 - - - -
190C GLY* 2.9 30.7 + - - +
387C ILE* 4.1 5.2 - - - +
388C PRO* 3.6 30.7 - - + -
390C ASN* 5.6 0.9 - - - +
391C ARG* 3.2 28.5 - - - +
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Residues in contact with ASP 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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150C GLY* 3.9 0.7 - - - -
151C LYS* 2.7 34.7 + - + +
152C ASP* 2.4 31.1 + - - +
154C GLN* 1.3 72.3 - - - +
156C ILE* 1.3 52.3 + - - +
158C ASN* 2.8 13.0 + - - +
159C LYS* 2.5 75.6 + - - +
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Residues in contact with ILE 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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148C ILE* 3.3 23.3 - - + +
149C THR* 3.8 4.0 - - - -
150C GLY 3.6 14.1 - - - +
152C ASP 3.4 10.9 + - - +
153C CYS* 3.2 11.1 + - - +
154C GLN 3.2 0.6 - - - -
155C ASP* 1.3 76.7 - - - +
157C ALA* 1.3 62.1 + - - +
159C LYS* 3.2 17.4 + - - +
160C GLY 3.3 6.9 + - - -
161C ALA* 3.3 21.6 + - + +
167C TYR* 3.3 58.3 - - + -
168C PHE 3.8 10.3 - - - +
169C ILE* 4.3 5.4 - - + -
182C CYS* 4.6 2.2 - - - -
184C ILE* 4.5 4.0 - - + -
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Residues in contact with ALA 157 (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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153C CYS 3.0 11.0 + - - +
154C GLN* 2.7 18.0 + - - +
156C ILE* 1.3 74.3 - - - +
158C ASN* 1.3 53.2 + - - +
160C GLY* 2.7 25.6 + - - -
161C ALA* 3.6 13.9 + - - +
162C LYS* 5.5 1.6 - - - -
184C ILE* 4.5 9.6 - - + -
188C GLY* 3.3 35.4 - - - +
190C GLY* 4.0 8.7 - - - +
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Residues in contact with ASN 158 (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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154C GLN* 2.7 38.4 + - - +
155C ASP* 2.8 14.0 + - - +
157C ALA* 1.3 73.4 - - - +
159C LYS* 1.3 60.0 + - + +
160C GLY* 2.7 11.1 + - - -
391C ARG* 3.0 30.9 + - - +
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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
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148C ILE* 4.1 22.3 - - + +
149C THR 3.3 27.4 + - - +
150C GLY* 4.1 2.0 - - - -
151C LYS* 5.2 3.6 - - - +
155C ASP* 2.5 60.9 + - - +
156C ILE 3.3 7.9 - - - +
158C ASN* 1.3 70.8 - - + +
160C GLY* 1.3 63.2 + - - +
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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