Contacts of the helix formed by residues 159 - 164 (chain C) in PDB entry 1GXD
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 GLY 159 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ASP* 2.9 16.1 - - - +
154C GLU* 3.5 18.6 - - - -
156C ASN 4.6 0.2 - - - -
157C ILE 3.0 5.3 + - - -
158C ASN* 1.3 73.6 - - - +
160C HIS* 1.3 55.4 + - - +
161C GLN 3.2 0.2 - - - -
162C ALA* 2.4 34.6 + - - +
163C LYS* 2.9 16.7 + - - +
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Residues in contact with HIS 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ALA 5.3 0.6 + - - -
585A PRO* 5.1 15.2 - - + +
586A ASP* 4.6 20.2 - - - -
604A LYS* 5.1 11.2 - - - -
150C ASP* 5.6 0.4 - - - +
153C THR* 5.1 7.9 - - + -
154C GLU* 3.2 18.1 + - - +
159C GLY* 1.3 73.2 - - - +
161C GLN* 1.3 70.8 + - + +
162C ALA 2.8 0.3 + - - -
163C LYS* 2.8 9.9 + - - +
164C PHE* 2.8 51.9 + + + +
165C PHE* 3.4 30.0 - + - -
179C ARG* 5.2 6.9 + - - -
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Residues in contact with GLN 161 (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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583A ALA* 5.3 4.0 - - - +
7C HIS* 2.6 28.9 - - + -
147C LEU 2.7 27.8 + - - +
148C TRP* 2.9 27.4 - - + +
149C MET* 3.4 22.7 + - - +
150C ASP* 3.0 19.4 + - - +
159C GLY 2.8 3.0 + - - -
160C HIS* 1.3 80.2 - - + +
162C ALA* 1.3 49.0 + - - +
165C PHE* 2.7 51.0 + - + +
177C TRP* 3.8 20.5 - - + +
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Residues in contact with ALA 162 (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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7C HIS* 3.1 13.9 - - - +
8C PRO* 3.8 25.3 - - + +
114C GLN* 3.8 11.4 + - - +
122C TYR* 3.9 15.2 + - - -
148C TRP* 4.5 3.4 - - + -
150C ASP* 3.5 4.4 + - - +
157C ILE 3.5 22.4 - - - +
158C ASN* 4.7 3.4 - - - +
159C GLY 2.4 27.3 + - - +
161C GLN* 1.3 69.7 - - - +
163C LYS* 1.3 63.6 + - - +
164C PHE 3.3 0.6 + - - -
165C PHE 4.1 1.9 + - - -
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Residues in contact with LYS 163 (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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111C SER* 3.0 14.1 + - - +
113C THR* 3.0 16.8 + - - -
114C GLN* 3.1 22.2 - - - +
158C ASN* 3.0 44.3 + - - +
159C GLY* 2.9 19.7 + - - +
160C HIS* 2.8 6.3 + - - +
162C ALA* 1.3 79.1 - - - +
164C PHE* 1.3 82.9 + - + +
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Residues in contact with PHE 164 (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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111C SER* 4.8 11.2 - - - -
113C THR* 3.8 34.6 - - + +
121C ARG* 5.6 1.2 + - - -
160C HIS* 2.8 36.6 + + + +
163C LYS* 1.3 102.0 - - + +
165C PHE* 1.3 65.7 + - + +
178C TYR 3.5 13.0 - - - +
179C ARG* 4.4 22.1 - - + +
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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