Contacts of the helix formed by residues 120 - 130 (chain A) in PDB entry 3CBG
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 PRO 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLN* 3.4 25.8 - - + +
119A GLY* 1.3 81.3 - - - +
121A ALA* 1.3 65.9 + - - +
122A LEU* 3.2 3.6 - - + +
123A ALA* 3.1 28.6 + - + +
124A THR* 3.3 9.7 + - - -
301A SAH 3.6 12.3 - - - +
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Residues in contact with ALA 121 (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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67A ILE* 3.8 18.4 - - + -
91A CYS* 4.5 10.0 - - + -
119A GLY 3.2 3.0 + - - -
120A PRO* 1.3 70.7 - - - +
122A LEU* 1.3 58.0 + - - +
124A THR* 3.1 9.4 + - - -
125A LEU* 2.9 33.3 + - + +
152A TYR* 3.6 23.8 - - + +
301A SAH 2.8 29.5 + - + +
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Residues in contact with LEU 122 (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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120A PRO* 3.2 4.8 + - + +
121A ALA* 1.3 75.6 - - - +
123A ALA* 1.3 56.2 + - - +
125A LEU* 3.3 4.9 + - + +
126A GLU* 2.9 31.3 + - - +
148A ASN* 4.2 23.6 - - + +
151A ARG* 4.0 27.6 - - + +
152A TYR* 3.6 30.5 + - + +
155A ILE* 4.1 18.6 - - + +
301A SAH 6.1 0.9 - - - +
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Residues in contact with ALA 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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119A GLY 5.7 0.2 - - - -
120A PRO* 3.1 25.2 + - + +
122A LEU* 1.3 78.4 - - - +
124A THR* 1.3 61.4 + - - +
126A GLU* 3.4 11.2 + - - +
127A GLN* 3.1 30.8 + - + +
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Residues in contact with THR 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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91A CYS* 3.6 28.9 - - - -
117A ARG* 3.6 39.0 + - + +
118A LEU 5.0 2.1 + - - -
119A GLY 4.3 5.5 + - - -
120A PRO 3.3 8.4 + - - -
121A ALA* 3.1 10.2 + - - -
123A ALA* 1.3 77.1 - - - +
125A LEU* 1.3 64.3 + - - +
127A GLN* 3.2 10.5 + - + +
128A LEU* 3.0 31.0 + - + +
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Residues in contact with LEU 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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65A LEU* 3.7 31.4 - - + -
67A ILE* 4.0 17.0 - - + -
91A CYS* 5.4 2.2 - - - -
121A ALA* 2.9 18.8 + - + +
122A LEU* 3.8 5.6 - - + +
124A THR* 1.3 74.5 - - - +
126A GLU* 1.3 64.7 + - - +
128A LEU* 3.2 13.7 + - + +
129A THR* 3.0 30.3 + - - +
152A TYR* 3.7 34.1 - - + +
155A ILE* 3.8 32.5 - - + -
156A GLY* 5.2 2.9 - - - -
159A LEU* 4.0 11.7 - - + -
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Residues in contact with GLU 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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122A LEU 2.9 17.0 + - - +
123A ALA* 3.4 11.1 - - - +
125A LEU* 1.3 77.9 - - - +
127A GLN* 1.3 61.0 + - - +
129A THR* 2.8 22.3 + - - +
130A GLN* 2.9 51.8 + - + +
155A ILE* 5.8 1.7 - - - +
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Residues in contact with GLN 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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117A ARG* 6.3 0.9 - - - +
123A ALA* 3.1 19.0 + - + +
124A THR* 3.6 9.9 - - + +
125A LEU 3.2 0.4 - - - -
126A GLU* 1.3 78.7 - - - +
128A LEU* 1.3 65.4 - - + +
130A GLN* 3.0 40.7 + - - +
131A GLY* 3.2 11.1 + - - -
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Residues in contact with LEU 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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65A LEU* 4.1 23.8 - - + -
89A ILE* 3.8 26.5 - - + -
117A ARG* 4.1 14.8 - - - +
124A THR* 3.0 29.6 + - + +
125A LEU* 3.5 28.3 - - + +
127A GLN* 1.3 78.8 - - + +
129A THR* 1.3 59.6 + - - +
131A GLY* 3.3 5.2 + - - -
135A PRO* 3.0 40.0 - - + +
137A PHE* 4.4 8.7 - - + -
159A LEU* 4.0 12.1 - - + -
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Residues in contact with THR 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 LEU 3.0 14.2 + - - +
126A GLU* 2.8 20.9 + - - +
128A LEU* 1.3 75.2 - - - +
130A GLN* 1.3 59.4 + - - +
131A GLY 3.1 6.8 + - - +
134A LEU* 3.7 23.2 - - + +
155A ILE* 4.0 15.5 - - + -
158A ASN* 4.4 6.7 - - - +
159A LEU* 3.7 25.6 - - + -
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Residues in contact with GLN 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 GLU* 2.9 54.3 + - + +
127A GLN* 3.0 28.3 + - - +
129A THR* 1.3 78.4 - - - +
131A GLY* 1.3 62.0 + - - +
132A LYS* 4.0 1.6 + - - +
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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