Contacts of the helix formed by residues 156 - 162 (chain A) in PDB entry 1GPU
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 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ASN* 4.0 12.8 - - - +
155A LEU* 1.3 75.6 - - - +
157A ASP* 1.3 66.5 + - - -
158A GLY 3.2 3.7 + - - -
159A CYS* 3.3 6.8 + - - +
160A LEU* 3.3 22.5 + - - +
184A TYR* 4.0 7.0 - - - -
185A ASP* 4.2 14.6 - - - -
1682A THD 4.3 12.1 - - - -
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Residues in contact with ASP 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLY* 1.3 71.3 - - - -
158A GLY* 1.3 62.3 + - - +
160A LEU* 3.2 4.2 + - - +
161A GLN* 3.1 28.8 + - - +
184A TYR* 2.4 36.1 + - - -
185A ASP 4.1 3.1 - - - +
186A ASP* 4.9 1.6 - - - +
187A ASN* 3.5 7.1 - - - +
188A LYS* 4.0 5.4 + - - -
190A THR* 3.8 13.5 - - + -
195A THR* 3.6 19.0 - - - +
199A PHE* 3.4 20.8 - - + -
1681A CA 2.5 22.0 - - - -
1682A THD 3.4 10.4 + - - +
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Residues in contact with GLY 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.9 18.8 - - - -
157A ASP* 1.3 79.3 - - - +
159A CYS* 1.3 60.5 + - - +
161A GLN* 3.2 11.6 + - - +
162A GLU* 3.3 18.2 + - - +
1682A THD 3.1 21.8 + - - -
416B ILE* 3.9 18.7 - - - +
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Residues in contact with CYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A SER* 3.1 49.8 - - - +
67A ASN* 4.1 3.6 - - - -
118A LEU* 3.8 10.7 - - - +
119A GLY* 3.4 24.9 - - - +
122A ILE* 4.6 2.0 - - + -
155A LEU* 4.0 18.4 - - + -
156A GLY 3.3 11.0 + - - +
158A GLY* 1.3 75.9 - - - +
160A LEU* 1.3 55.8 + - - +
161A GLN 3.3 0.5 + - - -
162A GLU* 3.4 8.7 + - - +
165A SER* 2.6 32.1 + - - -
1682A THD 4.3 0.4 + - - -
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Residues in contact with LEU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A LEU* 3.8 18.8 - - + -
156A GLY 3.3 7.8 + - - +
157A ASP* 3.2 10.0 + - - +
159A CYS* 1.3 78.2 - - - +
161A GLN* 1.3 59.7 + - - +
162A GLU 4.4 0.7 - - - +
165A SER* 3.7 8.8 + - - +
166A SER* 4.7 2.8 + - - -
184A TYR* 3.3 53.2 - - + +
199A PHE* 3.9 13.0 - - + -
201A GLU* 5.4 0.5 - - - +
203A VAL* 3.9 13.7 - - + -
206A ARG* 3.3 22.3 + - - +
207A TYR* 3.5 38.8 - - + +
243A LEU* 5.4 3.1 - - + -
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Residues in contact with GLN 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ASP 3.1 18.4 + - - +
158A GLY 3.8 3.6 - - - +
159A CYS 3.2 0.4 - - - -
160A LEU* 1.3 78.0 - - - +
162A GLU* 1.3 63.7 + - - +
163A GLY* 3.4 2.4 + - - -
190A THR* 4.1 10.5 + - - +
198A SER* 4.8 2.2 + - - -
199A PHE* 3.3 54.7 - - + +
167B GLU* 3.4 17.7 - - - +
415B GLY* 3.3 11.6 - - - -
416B ILE* 2.9 56.8 + - + +
417B ARG* 3.7 19.0 + - + +
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Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.5 24.5 - - + +
119A GLY* 4.3 0.2 - - - -
158A GLY 3.3 7.0 + - - +
159A CYS 3.4 8.0 + - - +
160A LEU 4.4 0.7 - - - +
161A GLN* 1.3 76.9 - - - +
163A GLY* 1.3 66.8 + - - +
164A ILE* 4.0 10.9 + - + -
165A SER* 3.0 24.3 + - - -
166A SER* 3.8 2.1 + - - -
1682A THD 3.1 10.2 - - - +
167B GLU* 3.7 12.3 - - - +
416B ILE* 3.1 34.4 - - + +
418B GLU* 2.5 29.9 + - - +
419B HIS 5.6 0.2 + - - -
448B TYR* 3.3 19.9 - - - -
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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