Contacts of the helix formed by residues 127 - 133 (chain C) in PDB entry 6PSI
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 LEU 127 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C THR* 1.3 74.9 - - - +
128C GLU* 1.3 71.9 + - - +
129C GLU 3.3 0.4 - - - -
130C ALA* 3.3 6.6 + - + +
131C PHE* 3.0 21.8 + - - +
153C VAL* 4.3 11.7 - - + +
180C LEU* 3.5 35.2 - - + -
183C HIS* 3.0 32.5 - - + +
184C PRO* 4.1 1.6 - - + -
185C VAL 3.6 2.2 - - - +
186C PHE* 3.5 51.6 - - + +
215C LEU* 3.8 12.8 - - + +
240C PHE* 3.5 13.2 - - + -
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Residues in contact with GLU 128 (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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168B VAL 5.4 0.4 - - - +
169B SER 5.3 1.6 - - - +
170B THR* 5.0 3.4 - - - -
171B ALA* 3.5 34.1 - - + +
126C THR* 3.4 13.9 - - + +
127C LEU* 1.3 77.5 - - - +
129C GLU* 1.4 66.5 + - - +
131C PHE* 3.3 9.8 - - - +
132C HIS* 3.0 31.7 + - - -
183C HIS* 3.1 38.3 + - - -
186C PHE* 4.5 2.4 - - - -
213C MET* 3.8 14.7 - - + +
215C LEU* 3.5 39.1 - - - +
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Residues in contact with GLU 129 (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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131B TRP* 4.5 7.4 - - - +
167B ASN* 2.9 46.8 + - - +
168B VAL 3.3 20.4 - - - +
169B SER* 3.3 27.1 + - - -
173B LEU* 5.1 0.2 - - - -
125C LEU* 3.8 14.6 - - + +
126C THR* 3.4 14.4 + - - +
127C LEU 3.3 0.4 - - - -
128C GLU* 1.4 78.4 - - - +
130C ALA* 1.3 59.8 + - - +
132C HIS* 2.9 38.9 + - - +
133C GLY* 2.9 25.9 + - - -
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Residues in contact with ALA 130 (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 LEU* 4.3 6.3 - - - -
126C THR 2.8 14.6 + - - +
127C LEU* 3.4 12.6 - - - +
128C GLU 3.3 0.2 - - - -
129C GLU* 1.3 77.1 - - - +
131C PHE* 1.4 59.9 - - - +
132C HIS 3.3 0.6 + - - -
133C GLY* 3.9 3.7 + - - -
151C PRO* 3.1 10.9 - - - +
152C GLY* 2.7 24.1 + - - +
153C VAL* 3.7 30.5 - - + +
240C PHE* 3.7 15.7 - - + -
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Residues in contact with PHE 131 (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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130B ALA* 5.5 5.2 - - + -
132B SER 3.9 4.0 - - - +
133B THR* 4.2 22.6 - - + -
127C LEU 3.0 13.7 + - - +
128C GLU 3.3 9.2 - - - +
130C ALA* 1.4 77.2 - - - +
132C HIS* 1.3 77.9 + + - +
151C PRO* 3.4 15.3 - - - +
215C LEU* 3.7 30.7 - - + -
216C GLU* 3.9 35.7 - - + -
239C GLY 4.2 10.1 - - - -
240C PHE* 3.3 12.3 - + + -
241C PRO* 3.7 34.6 - - + +
246C ARG* 4.3 9.2 - - - -
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Residues in contact with HIS 132 (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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130B ALA* 3.1 33.3 + - + +
131B TRP* 3.5 22.4 - - + +
132B SER 3.2 21.1 - - - +
167B ASN* 5.9 0.2 - - - +
171B ALA 2.9 28.8 + - - -
172B GLU* 3.7 17.7 - - - -
173B LEU 3.9 3.4 - - - -
128C GLU 3.0 17.9 + - - +
129C GLU* 2.9 36.8 + - - +
130C ALA 3.3 1.1 - - - -
131C PHE* 1.3 96.0 - + - +
133C GLY* 1.4 61.6 + - - +
134C GLY* 2.9 11.8 + - - -
151C PRO* 3.8 8.1 - - - +
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Residues in contact with GLY 133 (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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131B TRP* 3.3 10.1 + - - -
167B ASN* 5.8 0.7 - - - -
181B LEU* 4.7 13.9 - - - +
125C LEU* 6.0 0.4 - - - -
129C GLU 2.9 22.5 + - - -
130C ALA* 3.9 6.0 + - - -
132C HIS* 1.4 68.7 - - - +
134C GLY* 1.4 61.4 + - - -
136C ARG* 2.9 23.4 + - - +
149C ILE* 5.1 13.5 - - - -
151C PRO* 5.2 2.5 - - - -
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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