Contacts of the helix formed by residues 131 - 139 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86G ARG 4.5 1.7 - - - +
88G LYS* 3.6 36.7 + - + +
129G PRO* 3.7 22.6 - - - +
130G ASP* 1.3 72.5 + - - +
132G LEU* 1.3 61.5 + - - +
133G LEU 3.5 0.2 - - - -
134G PRO* 3.1 22.6 - - + +
135G VAL* 3.3 14.9 - - - +
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Residues in contact with LEU 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G THR* 3.2 31.0 - - - +
86G ARG* 4.0 10.1 - - - +
87G ASP 3.8 5.6 - - - +
88G LYS* 3.3 34.3 - - - +
91G LEU* 3.7 22.0 - - + -
115G VAL 5.4 0.2 - - - +
126G MET* 4.9 0.9 - - + -
128G VAL* 4.0 20.9 - - + -
129G PRO* 3.7 9.9 - - + +
130G ASP 2.7 6.7 + - - -
131G ASP* 1.3 81.4 - - - +
133G LEU* 1.3 64.6 + - - +
134G PRO 3.3 0.9 - - - -
135G VAL* 3.1 2.7 + - + +
136G TYR* 2.7 44.4 + - + -
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Residues in contact with LEU 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116G MET* 3.8 20.5 - - + -
126G MET* 4.4 8.8 - - + +
130G ASP* 2.9 8.0 + - + +
132G LEU* 1.3 77.7 - - - +
134G PRO* 1.3 61.1 - - + +
136G TYR 3.2 0.5 + - - -
137G ARG* 2.7 57.9 + - + +
156G LEU* 3.4 63.0 - - + +
157G LEU* 4.3 7.0 - - + -
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Residues in contact with PRO 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G ASP 3.2 12.6 - - - +
131G ASP* 3.1 23.8 - - + +
133G LEU* 1.3 93.1 - - + +
135G VAL* 1.3 53.1 + - + +
137G ARG* 3.1 23.3 + - - +
138G GLU* 2.7 46.4 + - - +
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Residues in contact with VAL 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88G LYS* 3.6 29.6 - - + +
91G LEU* 3.5 27.8 - - + -
92G ALA* 4.0 24.0 - - + +
131G ASP 3.3 19.3 - - - +
132G LEU* 3.1 6.2 + - - +
134G PRO* 1.3 76.9 - - + +
136G TYR* 1.3 57.4 + - - +
138G GLU* 5.4 0.2 - - - -
139G LYS* 2.9 38.8 + - + +
140G VAL* 3.1 9.6 + - + -
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Residues in contact with TYR 136 (chain G).
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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82G THR* 5.6 3.1 - - - -
83G GLY 3.2 24.8 + - - -
85G THR* 4.5 4.9 + - - -
91G LEU* 3.3 40.4 - - + +
112G CYS* 4.7 4.0 - - - -
113G ASP 4.2 3.7 + - - -
114G PRO* 3.8 23.8 - - + -
115G VAL 3.8 25.7 + - - -
116G MET* 3.8 21.3 - - + -
132G LEU* 2.7 36.5 + - + +
133G LEU 3.6 2.9 - - - +
135G VAL* 1.3 73.7 - - - +
137G ARG* 1.3 59.4 + - - +
140G VAL* 3.7 20.6 - - + -
141G VAL* 3.0 37.0 + - + +
157G LEU* 4.0 13.7 - - + -
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Residues in contact with ARG 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G LEU* 2.7 41.3 + - + +
134G PRO* 3.5 14.9 - - - +
136G TYR* 1.3 76.2 - - - +
138G GLU* 1.3 92.5 + - - +
141G VAL* 4.4 1.1 - - - -
142G PRO* 4.2 5.4 - - - +
156G LEU 4.5 7.3 + - - -
157G LEU* 3.2 43.6 + - - +
159G GLY* 5.5 2.5 - - - +
178G MET* 3.2 31.2 - - + +
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Residues in contact with GLU 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G PRO* 2.7 25.8 + - - +
137G ARG* 1.3 103.6 + - + +
139G LYS* 1.3 65.8 + - + +
142G PRO* 2.9 21.2 - - - +
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Residues in contact with LYS 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G ALA* 4.1 29.1 + - - +
95G VAL* 3.5 30.6 - - + +
96G ASP* 3.2 26.9 + - - -
99G GLN* 5.8 0.4 + - - -
135G VAL* 2.9 22.2 + - + +
138G GLU* 1.3 81.3 - - + +
140G VAL* 1.3 65.0 + - - +
142G PRO* 3.4 8.6 - - - +
143G VAL* 3.8 5.2 - - - +
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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