Contacts of the strand formed by residues 184 - 189 (chain F) in PDB entry 1R5I
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 LEU 184 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96F GLU* 4.3 15.0 - - + +
97F PRO* 3.6 39.0 - - + +
99F VAL* 4.2 17.9 - - + +
173F CYS 3.6 0.6 - - - +
174F GLN* 3.2 0.5 - - - -
175F VAL* 2.8 42.5 + - + +
180F VAL* 3.3 46.0 - - + -
182F SER 3.7 1.1 - - - +
183F PRO* 1.3 73.0 - - - +
185F THR* 1.3 66.7 + - - +
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Residues in contact with THR 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F THR* 3.7 25.4 - - + -
173F CYS 3.2 3.4 - - - -
174F GLN* 3.8 25.6 - - + +
183F PRO 4.3 6.0 + - - +
184F LEU* 1.3 84.7 - - - +
186F VAL* 1.3 68.7 + - - +
187F GLU* 4.3 1.8 - - - -
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Residues in contact with VAL 186 (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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99F VAL* 3.4 43.7 - - + +
100F THR* 4.6 1.3 - - - -
101F VAL* 3.4 39.0 - - + +
131F TRP* 5.1 0.3 - - - -
172F THR* 3.4 2.5 - - - -
173F CYS* 2.9 31.7 + - - +
185F THR* 1.3 79.1 - - - +
187F GLU* 1.3 72.7 + - - +
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Residues in contact with GLU 187 (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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101F VAL* 5.1 0.7 - - - +
170F VAL* 3.3 12.0 - - + +
171F TYR 3.3 4.5 - - - +
172F THR* 3.5 23.3 - - + +
185F THR* 6.0 1.8 - - - -
186F VAL* 1.3 87.4 - - - +
188F TRP* 1.3 67.2 + - - +
189F ARG* 3.3 36.3 + - + +
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Residues in contact with TRP 188 (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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101F VAL* 3.9 38.4 - - + -
103F PRO* 3.2 44.0 - - + -
115F LEU* 3.7 36.5 - - + +
131F TRP* 5.8 0.7 - - + -
165F PRO* 4.9 7.4 - - + +
170F VAL* 3.7 1.1 - - - -
171F TYR* 3.0 36.4 + + + +
187F GLU* 1.3 78.8 - - - +
189F ARG* 1.3 78.7 + - - +
190F ALA* 3.4 9.4 + - - +
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Residues in contact with ARG 189 (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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169F GLU 4.0 3.6 - - - -
170F VAL* 3.2 36.8 - - - +
187F GLU* 3.3 21.6 + - + +
188F TRP* 1.3 85.0 + - - +
190F ALA* 1.3 70.6 + - - +
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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