Contacts of the helix formed by residues 139 - 144 (chain F) 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 LYS 139 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92F ALA* 4.3 27.5 + - - +
95F VAL* 3.7 23.0 - - + +
96F ASP* 3.2 25.9 + - - -
99F GLN* 5.7 0.6 + - - -
135F VAL* 2.8 23.3 + - + +
138F GLU* 1.3 83.3 - - + +
140F VAL* 1.3 67.8 + - - +
142F PRO* 3.5 8.4 - - - +
143F VAL* 3.7 12.6 - - - +
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Residues in contact with VAL 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LEU* 3.8 24.9 - - + -
95F VAL* 3.7 22.0 - - + -
110F TYR* 3.4 28.9 - - + +
112F CYS* 3.7 20.9 - - - -
135F VAL* 3.1 13.9 + - + +
136F TYR* 3.4 22.0 + - + +
139F LYS* 1.3 73.9 - - - +
141F VAL* 1.3 69.9 + - + +
142F PRO* 3.0 2.0 - - - -
143F VAL* 2.9 23.2 + - - +
144F ALA 3.2 4.0 + - - -
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Residues in contact with VAL 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F CYS* 5.8 0.9 - - - -
114F PRO* 5.7 2.0 - - + -
136F TYR* 3.0 22.3 + - + +
137F ARG* 4.4 6.5 - - - +
140F VAL* 1.3 75.2 - - + +
142F PRO* 1.3 72.6 - - + +
144F ALA* 2.9 18.2 + - - +
147F ILE* 4.6 15.7 - - + -
157F LEU* 4.0 26.7 - - + -
175F LEU* 4.5 3.1 - - + +
178F MET* 3.8 25.4 - - + -
180F PRO* 3.4 33.4 - - + +
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Residues in contact with PRO 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F ARG 4.0 6.7 - - - +
138F GLU* 3.0 29.6 - - - +
139F LYS 3.5 4.5 - - - +
140F VAL 3.0 13.9 - - - +
141F VAL* 1.3 94.7 - - + +
143F VAL* 1.3 58.4 + - + +
144F ALA 3.6 0.2 + - - -
178F MET* 3.0 19.4 - - + +
179F GLY* 3.5 17.0 - - - -
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Residues in contact with VAL 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F VAL* 4.2 12.3 - - + -
98F VAL* 4.4 8.7 - - + -
99F GLN* 4.1 31.4 - - + +
102F LYS* 3.6 34.0 - - + -
110F TYR* 3.7 20.3 - - + -
139F LYS 3.7 13.7 - - - +
140F VAL* 2.9 22.3 + - - +
142F PRO* 1.3 80.2 - - + +
144F ALA* 1.3 58.2 + - - +
145F ASP* 4.5 0.6 - - - +
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Residues in contact with ALA 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F TYR* 3.9 10.1 - - + +
112F CYS* 3.8 29.4 - - + -
140F VAL 3.2 8.1 + - - +
141F VAL* 2.9 13.9 + - - +
142F PRO 4.5 0.2 - - - +
143F VAL* 1.3 78.0 - - - +
145F ASP* 1.3 62.2 + - - +
146F ILE 4.4 1.6 - - - +
147F ILE* 4.1 16.6 - - + -
179F GLY 3.6 3.1 - - - +
180F PRO* 2.9 27.4 - - + +
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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