Contacts of the helix formed by residues 122 - 130 (chain A) in PDB entry 4G17
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 SER 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A PRO* 1.3 74.3 - - - +
123A LEU* 1.3 64.3 + - - +
124A GLU* 3.4 9.9 + - - +
125A ASP* 3.0 34.3 + - - +
126A LEU* 3.0 25.6 + - - +
165A PRO 3.7 2.7 - - - -
166A GLU* 3.6 28.2 - - - +
168A PHE 3.1 9.6 - - - -
169A LEU* 3.8 9.9 - - - +
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Residues in contact with LEU 123 (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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122A SER* 1.3 73.1 - - - +
124A GLU* 1.3 56.2 + - - +
126A LEU* 3.8 11.1 - - + +
127A PHE* 2.8 30.1 + - - +
134A PHE* 3.9 4.4 - - + -
142A ILE* 4.0 32.3 - - + -
146A LEU* 4.6 0.2 - - + -
165A PRO* 3.3 10.9 + - - +
168A PHE* 2.8 40.1 + - + +
170A ILE* 4.9 1.8 - - + +
181A ILE* 4.4 15.7 - - + -
238A MET* 4.4 4.3 - - + -
242A PHE* 4.0 26.5 - - + -
325A TRP* 3.9 29.4 - - + -
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Residues in contact with GLU 124 (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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122A SER* 3.2 8.8 + - - +
123A LEU* 1.3 79.1 - - - +
125A ASP* 1.3 63.7 + - - +
127A PHE* 3.3 6.7 + - - +
128A ASP* 3.0 30.0 + - - +
132A ARG* 3.0 29.3 + - - -
165A PRO* 3.3 30.9 + - + +
166A GLU* 3.9 30.2 - - + +
214A ARG* 5.0 2.4 + - - -
215A TYR* 4.3 2.1 + - - -
241A TYR* 3.1 22.1 + - - -
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Residues in contact with ASP 125 (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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121A PRO* 4.0 12.3 - - + -
122A SER* 3.0 33.5 + - - +
124A GLU* 1.3 80.6 - - - +
126A LEU* 1.3 62.2 + - - +
128A ASP* 3.5 9.4 + - - +
129A LEU* 3.1 22.6 + - - +
331A PRO* 4.8 9.5 - - + +
401A 0VN 3.8 24.7 - - - +
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Residues in contact with LEU 126 (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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121A PRO* 3.7 26.9 - - + +
122A SER 3.0 16.2 + - - +
123A LEU* 3.8 11.0 - - + +
125A ASP* 1.3 73.4 - - - +
127A PHE* 1.3 67.9 + - - +
129A LEU* 3.0 10.3 + - + +
130A CYS* 2.9 26.2 + - - -
134A PHE* 4.0 3.1 - - + -
170A ILE* 3.7 24.2 - - + -
325A TRP* 3.6 62.1 - - + +
330A LEU* 4.3 14.1 - - + -
331A PRO* 5.8 0.4 - - + -
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Residues in contact with PHE 127 (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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123A LEU 2.8 19.0 + - - +
124A GLU* 3.4 9.6 - - - +
126A LEU* 1.3 75.8 - - - +
128A ASP* 1.3 56.3 + - - +
130A CYS* 3.0 9.5 + - - +
132A ARG* 2.8 74.9 + - + -
133A THR* 3.0 29.4 - - - -
134A PHE* 3.5 27.5 - + + -
241A TYR* 3.7 53.4 - + - -
242A PHE* 3.5 23.3 - + + -
245A GLY* 4.0 5.6 - - - -
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Residues in contact with ASP 128 (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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124A GLU* 3.0 20.1 + - - +
125A ASP* 3.7 11.5 - - - +
127A PHE* 1.3 76.8 - - - +
129A LEU* 1.3 63.0 + - - +
131A ASP* 3.1 16.5 + - - +
132A ARG* 2.6 43.5 + - - +
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Residues in contact with LEU 129 (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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125A ASP 3.1 10.6 + - - +
126A LEU* 3.0 21.7 + - + +
128A ASP* 1.3 80.0 - - - +
130A CYS* 1.3 57.9 - - - +
131A ASP* 3.3 7.3 + - - +
325A TRP* 5.1 2.2 - - + -
328A LYS* 4.0 29.0 - - + -
329A GLN 3.8 14.6 - - - +
330A LEU* 3.3 34.1 - - + -
331A PRO* 4.1 13.0 - - + -
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Residues in contact with CYS 130 (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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126A LEU 2.9 16.6 + - - +
127A PHE 3.0 4.0 + - - +
129A LEU* 1.3 78.8 - - - +
131A ASP* 1.3 72.8 + - - +
132A ARG 3.2 2.4 + - - -
133A THR* 3.5 21.7 + - - +
134A PHE* 3.9 16.8 - - + -
324A ASP* 3.8 16.2 - - + -
325A TRP* 3.8 37.9 - - - -
328A LYS* 4.6 8.5 - - - +
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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