Contacts of the helix formed by residues 129 - 138 (chain A) in PDB entry 3FRR
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A CYS* 2.8 18.9 + - - +
126A ALA 4.2 2.6 + - - -
127A LYS 3.5 2.4 + - - -
128A TYR* 1.3 89.2 + - - +
130A LYS* 1.3 59.5 + - - +
131A GLU* 3.9 19.3 + - - +
132A TYR* 3.2 17.5 + - - +
133A GLY* 3.0 23.0 + - - -
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Residues in contact with LYS 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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125A CYS* 3.6 15.9 + - + +
126A ALA* 6.4 0.2 - - - -
129A SER* 1.3 70.2 - - - +
131A GLU* 1.3 69.3 + - - +
133A GLY* 3.3 1.5 + - - +
134A LYS* 2.9 54.0 + - - +
137A ARG* 4.6 7.6 + - - +
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Residues in contact with GLU 131 (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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129A SER* 3.2 15.7 - - - +
130A LYS* 1.3 85.6 + - - +
132A TYR* 1.3 65.0 + - - +
134A LYS* 3.4 17.2 + - - +
135A LEU* 3.3 28.0 + - + +
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Residues in contact with TYR 132 (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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92A LEU* 3.3 30.3 - - + +
97A ALA* 3.9 0.5 + - - +
100A VAL* 3.9 8.8 - - + +
101A SER* 2.5 27.5 + - - -
104A ILE* 3.8 17.7 - - + -
124A LEU 5.2 0.2 - - - -
125A CYS* 5.8 0.2 - - - -
128A TYR* 3.3 42.2 - - + +
129A SER* 3.2 7.1 + - - +
131A GLU* 1.3 80.0 - - - +
133A GLY* 1.3 62.4 + - - +
135A LEU* 3.1 11.8 + - + +
136A CYS* 3.0 41.9 + - - -
141A ILE* 3.7 29.6 - - + -
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Residues in contact with GLY 133 (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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104A ILE* 3.6 10.9 - - - +
125A CYS* 3.5 29.4 - - - -
129A SER 3.0 10.7 + - - -
130A LYS 3.3 4.4 + - - -
132A TYR* 1.3 79.6 - - - +
134A LYS* 1.3 55.8 + - - +
136A CYS* 3.3 3.4 + - - +
137A ARG* 3.0 34.3 + - - +
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Residues in contact with LYS 134 (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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130A LYS* 2.9 46.4 + - - +
131A GLU* 3.9 15.1 - - - +
132A TYR 3.3 0.4 - - - -
133A GLY* 1.3 76.5 - - - +
135A LEU* 1.3 64.0 + - + +
137A ARG* 3.4 31.8 + - - +
138A THR* 3.3 21.5 + - - +
140A GLN* 4.0 2.0 - - - +
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A GLU* 3.3 15.4 + - + +
132A TYR* 3.1 11.9 + - - +
134A LYS* 1.3 77.6 - - + +
136A CYS* 1.3 60.2 + - - +
138A THR* 3.8 2.5 - - - -
139A ASN* 3.3 1.4 + - - -
140A GLN* 3.0 59.5 + - + +
141A ILE* 3.0 35.8 + - + +
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Residues in contact with CYS 136 (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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101A SER* 3.5 25.4 - - - +
104A ILE* 3.6 20.6 - - + -
105A TRP* 3.2 18.4 - - - +
132A TYR* 3.0 56.4 + - - -
133A GLY 3.6 7.6 - - - +
134A LYS 3.2 0.2 - - - -
135A LEU* 1.3 74.7 - - - +
137A ARG* 1.3 59.4 + - - +
138A THR 3.1 2.5 - - - -
139A ASN* 3.0 15.6 + - - -
141A ILE* 3.7 10.1 - - - -
144A VAL* 3.8 2.1 - - - +
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Residues in contact with ARG 137 (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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104A ILE* 3.7 22.3 + - + +
105A TRP* 3.2 9.6 - - - +
108A PRO* 3.9 23.5 - - + +
109A ARG* 3.0 28.6 + - - +
121A ALA* 5.6 3.6 - - - +
122A ASP* 5.3 5.9 + - - -
125A CYS* 3.9 24.5 - - - -
130A LYS* 4.6 9.1 + - - +
133A GLY* 3.0 15.7 + - - +
134A LYS* 3.4 39.4 + - - +
136A CYS* 1.3 75.2 - - - +
138A THR* 1.3 60.8 + - + +
139A ASN 3.5 0.2 - - - -
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Residues in contact with THR 138 (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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105A TRP* 4.3 4.5 - - - +
109A ARG* 5.3 1.3 - - - +
134A LYS 3.3 14.0 + - - +
135A LEU 3.3 1.7 + - - -
137A ARG* 1.3 80.2 - - + +
139A ASN* 1.3 66.5 + - - +
140A GLN* 2.6 42.8 + - - +
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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