Contacts of the helix formed by residues 127 - 139 (chain D) in PDB entry 5GQQ
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 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C GLU* 2.5 33.0 + - - -
126D LEU* 1.3 73.1 - - - +
128D ASP* 1.3 62.7 + - - +
129D GLN* 3.6 7.5 + - - +
130D PHE* 3.1 24.3 + - - +
131D HIS* 2.9 18.9 + - - -
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Residues in contact with ASP 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LYS* 3.9 18.1 - - - +
116D LYS* 4.1 27.3 + - - +
126D LEU 3.8 0.6 + - - -
127D SER* 1.3 74.0 - - - +
129D GLN* 1.3 73.5 + - + +
130D PHE 3.4 0.5 + - - -
131D HIS* 3.4 20.0 + - - +
132D ASP* 3.4 10.9 - - - +
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Residues in contact with GLN 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LYS* 4.9 2.9 + - - -
127D SER* 3.2 6.8 + - - +
128D ASP* 1.3 88.9 - - + +
130D PHE* 1.3 61.0 + - - +
132D ASP* 3.7 25.3 + - - +
133D ILE* 3.7 17.7 - - - +
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Residues in contact with PHE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C GLU* 3.3 39.9 - - + +
184C LEU* 3.4 31.0 - - + -
185C SER* 4.3 10.3 - - - -
188C PHE* 5.2 0.2 - + - -
126D LEU* 3.7 36.1 - - + -
127D SER* 3.1 22.4 + - - +
128D ASP 3.2 0.2 - - - -
129D GLN* 1.3 75.1 - - - +
131D HIS* 1.3 59.7 + - - +
132D ASP 3.1 2.2 - - - -
133D ILE* 2.8 37.5 + - + +
134D LEU* 3.0 46.5 + - + -
158D LEU* 5.1 2.7 - - + -
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Residues in contact with HIS 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LYS* 4.4 18.8 - - + -
115D LEU* 4.5 9.4 - - + +
116D LYS* 3.6 52.8 + - + +
119D LEU* 4.2 24.9 - - + +
126D LEU* 3.6 32.2 - - + +
127D SER 2.9 25.0 + - - -
128D ASP* 3.4 13.6 + - - +
130D PHE* 1.3 78.0 - - - +
132D ASP* 1.3 60.6 + - - +
134D LEU* 3.9 6.5 - - + +
135D ILE* 3.1 29.9 + - - +
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Residues in contact with ASP 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LYS* 2.9 40.3 + - - +
128D ASP 3.4 9.5 - - - +
129D GLN* 3.7 28.4 + - - +
130D PHE 3.1 0.6 - - - -
131D HIS* 1.3 77.7 - - - +
133D ILE* 1.3 62.0 + - + +
135D ILE* 4.0 7.3 + - - +
136D ARG* 3.5 32.0 + - - +
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Residues in contact with ILE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C SER* 4.4 28.5 - - - -
188C PHE* 6.0 2.2 - - + -
129D GLN 3.7 16.4 - - - +
130D PHE* 2.8 28.1 + - + +
132D ASP* 1.3 77.8 - - + +
134D LEU* 1.3 64.8 + - + +
136D ARG* 3.2 14.5 + - + +
137D LYS* 3.0 37.5 + - + +
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C PHE* 3.6 26.5 - - + -
115D LEU* 4.3 7.4 - - + -
119D LEU* 3.5 31.9 - - + -
126D LEU* 3.9 3.4 - - + -
130D PHE* 3.0 47.7 + - + +
131D HIS* 3.4 9.4 + - - +
133D ILE* 1.3 74.5 - - + +
135D ILE* 1.3 58.6 + - - +
137D LYS* 2.9 3.8 + - + +
138D PHE* 2.6 69.3 + - + -
158D LEU* 4.5 6.3 - - + -
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Residues in contact with ILE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ASP* 4.0 3.6 - - - -
112D LYS* 3.5 40.6 - - + +
115D LEU* 4.1 8.9 - - + +
131D HIS 3.1 17.3 + - - +
132D ASP* 4.1 8.3 - - - +
134D LEU* 1.3 77.7 - - - +
136D ARG* 1.3 60.0 + - + +
138D PHE* 4.0 0.3 - - - +
139D ASP* 3.1 32.0 + - + +
144D GLY* 3.5 37.2 - - - +
146D ILE* 4.0 25.6 - - + +
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Residues in contact with ARG 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ASP* 3.5 29.9 + - - +
133D ILE* 3.2 15.8 + - - +
134D LEU 3.1 0.8 - - - -
135D ILE* 1.3 83.7 - - + +
137D LYS* 1.3 67.6 + - + +
139D ASP* 4.4 10.9 - - - +
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Residues in contact with LYS 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C SER 5.0 3.1 + - - -
188C PHE* 3.7 56.6 - - + -
189C SER* 3.8 29.1 - - - +
133D ILE* 3.0 23.8 + - + +
134D LEU* 2.9 9.2 + - - +
136D ARG* 1.3 86.7 - - + +
138D PHE* 1.3 64.4 + - - +
139D ASP 3.5 3.1 - - - +
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Residues in contact with PHE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C PHE* 3.7 13.5 - + - -
61D ASN* 5.5 0.7 + - - -
115D LEU* 4.5 19.3 - - + -
119D LEU* 5.3 1.8 - - + -
134D LEU* 2.6 64.5 + - + +
135D ILE 4.0 0.2 - - - +
137D LYS* 1.3 77.4 - - - +
139D ASP* 1.3 64.2 + - - +
140D ARG* 4.2 2.8 - - - +
146D ILE* 3.6 36.6 - - + -
150D ASP* 3.2 31.3 - - - +
151D PHE* 4.6 5.6 - + - -
153D GLN* 6.0 0.5 - - - +
154D GLY* 3.5 43.7 - - - -
155D CYS* 4.1 7.4 - - - -
158D LEU* 4.8 7.0 - - + -
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Residues in contact with ASP 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ILE* 3.1 18.0 + - + +
136D ARG* 4.4 10.0 - - - +
137D LYS 3.5 4.0 - - - +
138D PHE* 1.3 85.0 - - - +
140D ARG* 1.3 66.0 + - - +
141D GLN* 2.4 39.2 + - - +
142D GLY* 3.2 14.5 + - - -
143D ARG 3.2 1.4 + - - -
144D GLY* 3.1 28.4 + - - -
145D GLN 3.3 20.4 + - - +
146D ILE* 5.2 2.5 - - + -
150D ASP* 3.8 5.6 - - - +
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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