Contacts of the helix formed by residues 131 - 139 (chain D) in PDB entry 1RFU
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 ASP 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A GLN* 4.6 20.5 + - + +
220A ARG* 5.1 4.2 + - - -
86D ARG 4.5 1.9 - - - +
88D LYS* 3.7 34.7 + - + +
129D PRO* 3.6 23.6 - - - +
130D ASP* 1.3 71.8 + - - +
132D LEU* 1.3 62.4 + - - +
134D PRO* 3.0 22.8 - - - +
135D VAL* 3.4 13.9 - - - +
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Residues in contact with LEU 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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85D THR* 3.3 28.3 - - - +
86D ARG* 3.9 14.6 - - - +
87D ASP 3.7 5.8 - - - +
88D LYS* 3.3 33.9 - - - +
91D LEU* 3.7 22.0 - - + -
116D MET* 5.2 0.2 - - + -
126D MET* 5.0 3.6 - - + -
128D VAL* 4.0 12.8 - - + -
129D PRO* 3.7 15.3 - - + +
130D ASP 2.7 6.7 + - - -
131D ASP* 1.3 79.7 - - - +
133D LEU* 1.3 64.6 + - - +
134D PRO 3.2 2.0 - - - -
135D VAL* 3.0 3.7 + - + +
136D TYR* 2.7 43.4 + - + -
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Residues in contact with LEU 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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116D MET* 3.8 19.3 - - + -
126D MET* 4.4 8.8 - - + +
130D ASP* 2.9 9.1 + - + +
132D LEU* 1.3 77.4 - - - +
134D PRO* 1.3 66.5 - - + +
136D TYR* 3.7 0.5 - - - +
137D ARG* 2.8 46.4 + - + +
156D LEU* 3.4 65.7 - - + +
157D LEU* 4.2 5.8 - - + -
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Residues in contact with PRO 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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130D ASP 3.1 13.0 - - - +
131D ASP* 3.0 25.4 - - + +
132D LEU 3.4 0.2 - - - -
133D LEU* 1.3 93.1 - - + +
135D VAL* 1.3 56.7 + - + +
137D ARG* 3.6 23.1 - - - +
138D GLU* 2.8 41.3 + - - +
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Residues in contact with VAL 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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88D LYS* 3.6 30.3 - - + -
91D LEU* 3.4 30.3 - - + -
92D ALA* 4.0 21.8 - - + +
131D ASP 3.4 18.2 - - - +
132D LEU* 3.0 7.0 + - - +
134D PRO* 1.3 77.9 - - + +
136D TYR* 1.3 59.4 + - - +
138D GLU* 5.4 0.2 - - - -
139D LYS* 2.8 39.6 + - + +
140D VAL* 3.1 9.6 + - + -
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Residues in contact with TYR 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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82D THR* 5.6 3.3 - - - -
83D GLY* 3.3 24.3 + - - -
85D THR* 4.7 5.3 + - - -
91D LEU* 3.3 37.7 - - + +
112D CYS* 4.5 7.9 - - - -
113D ASP 4.1 3.1 + - - -
114D PRO* 3.8 24.5 - - + -
115D VAL 3.7 19.3 + - - -
116D MET* 3.8 28.0 - - + -
132D LEU* 2.7 36.4 + - + +
133D LEU 3.7 3.4 - - - +
135D VAL* 1.3 74.1 - - - +
137D ARG* 1.3 58.6 + - - +
140D VAL* 3.5 18.6 + - + -
141D VAL* 2.9 36.6 + - + +
157D LEU* 4.1 13.5 - - + -
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Residues in contact with ARG 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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133D LEU* 2.8 35.6 + - + +
134D PRO* 3.9 18.6 - - - +
136D TYR* 1.3 79.8 - - - +
138D GLU* 1.3 92.5 + - - +
141D VAL* 4.6 1.3 - - - -
142D PRO* 4.2 5.5 - - - +
156D LEU 4.6 6.1 + - - -
157D LEU* 3.2 41.5 + - - +
159D GLY* 5.7 2.2 - - - +
178D MET* 3.2 31.3 - - + +
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Residues in contact with GLU 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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134D PRO* 2.8 23.1 + - - +
135D VAL* 5.4 0.2 - - - -
137D ARG* 1.3 106.7 + - - +
139D LYS* 1.3 66.0 + - + +
142D PRO* 3.1 17.4 - - - +
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Residues in contact with LYS 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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92D ALA* 4.1 30.0 + - - +
95D VAL* 3.7 21.3 - - + +
96D ASP* 3.2 27.5 + - - -
135D VAL* 2.8 23.1 + - + +
138D GLU* 1.3 80.0 - - + +
140D VAL* 1.3 67.3 + - - +
142D PRO* 3.4 9.1 - - - +
143D VAL* 3.7 12.3 - - - +
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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