Contacts of the strand formed by residues 186 - 191 (chain C) in PDB entry 4FQX
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 THR 186 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A THR 3.8 5.0 + - - -
130A THR* 3.4 14.7 - - + +
131A GLY* 3.1 34.7 + - - -
132A VAL 4.3 1.0 + - - +
177C ILE* 4.1 16.2 - - + -
178C VAL 3.2 4.0 - - - -
179C THR* 3.5 25.4 - - + +
184C ARG 3.5 10.7 + - - +
185C TYR* 1.3 96.7 - - - +
187C ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLY* 4.5 2.9 - - - -
101C PRO* 3.7 24.9 - - + +
102C ILE* 5.0 0.7 - - - -
103C ALA* 4.9 9.9 - - - +
176C CYS 3.6 0.9 - - - +
177C ILE* 3.3 5.5 - - - +
178C VAL* 2.8 45.9 + - + +
185C TYR* 4.1 12.5 - - + +
186C THR* 1.3 75.6 - - - +
188C ILE* 1.3 62.8 + - - +
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Residues in contact with ILE 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A THR* 4.7 8.7 - - + +
131A GLY* 3.8 23.6 + - - -
151A LEU* 5.7 0.2 - - + -
152A PRO* 4.0 39.9 - - + +
103C ALA* 5.0 3.2 + - - +
175C SER* 4.1 15.9 - - - -
176C CYS 3.3 9.2 - - - +
177C ILE* 3.8 24.0 - - + -
187C ALA* 1.3 77.8 - - - +
189C ALA* 1.3 67.8 + - - +
190C TYR* 3.7 29.4 - - + +
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Residues in contact with ALA 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PRO* 5.9 0.2 - - - -
103C ALA* 3.6 30.3 - - + +
104C GLU* 4.4 2.2 - - - -
105C VAL* 3.8 25.5 - - + +
175C SER* 3.3 2.2 - - - -
176C CYS 2.9 31.9 + - - +
188C ILE* 1.3 77.4 - - - +
190C TYR* 1.3 65.2 + - - +
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Residues in contact with TYR 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PRO* 3.8 30.5 - - + +
123A ARG* 4.4 11.6 + - - -
152A PRO* 3.6 30.0 + - + -
153A PHE* 3.7 22.2 - - - -
154A LEU* 4.4 21.2 + - + -
105C VAL* 4.5 7.2 + - - +
139C SER* 6.5 0.4 - - - -
173C ILE* 4.6 11.9 - - + -
174C PHE 3.3 13.5 - - - -
175C SER* 4.1 9.9 - - - -
188C ILE* 3.7 31.2 - - + +
189C ALA* 1.3 78.0 - - - +
191C TRP* 1.3 63.9 + - - +
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Residues in contact with TRP 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PRO* 5.1 0.4 - - - -
105C VAL* 3.6 44.6 - - + -
106C PHE* 4.3 2.6 - - - +
107C THR* 3.6 29.1 + - + +
111C LEU* 4.3 18.2 - - + -
119C LEU* 3.8 12.0 - - + +
166C PHE* 3.7 28.9 - + - -
168C PRO* 4.4 1.3 - - + -
172C ASP* 4.1 11.4 - - + -
173C ILE* 3.4 1.6 - - - +
174C PHE* 2.8 53.8 + + + +
190C TYR* 1.3 76.4 - - - +
192C VAL* 1.3 83.5 + - - +
193C PRO* 4.0 28.7 - - + -
194C ARG 5.3 0.4 - - - -
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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