Contacts of the strand formed by residues 181 - 185 (chain A) in PDB entry 2FQ6
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 ILE 181 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE* 3.7 32.3 - - + -
149A LYS* 2.8 22.5 + - + +
150A ILE* 3.4 7.5 - - + +
151A VAL 3.0 22.3 + - - +
179A ASP 3.8 5.2 - - - +
180A ALA* 1.3 72.5 - - - +
182A ILE* 1.3 63.1 + - - +
183A MET* 3.6 33.0 + - + -
202A ASP* 3.6 17.7 - - + -
203A VAL* 4.1 7.2 - - + -
228A ARG* 3.7 22.7 - - - +
229A CYS* 3.8 20.6 - - - -
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Residues in contact with ILE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL* 3.4 18.4 - - + +
153A LEU* 3.9 27.4 - - + -
169A ILE* 5.6 1.3 - - + -
170A VAL* 4.0 23.3 - - + -
173A VAL* 3.8 33.9 - - + -
174A ARG* 3.6 34.1 - - - +
180A ALA 4.5 0.2 - - - +
181A ILE* 1.3 73.3 - - - +
183A MET* 1.3 63.1 + - - +
200A GLY 4.3 0.7 - - - +
201A ILE* 3.3 12.4 - - + +
202A ASP* 2.7 42.8 + - - +
203A VAL 3.2 6.6 + - - -
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Residues in contact with MET 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A SER* 3.3 39.0 - - - +
94A ILE* 4.1 21.1 - - - -
97A PHE* 3.5 22.4 - - + -
150A ILE* 3.5 25.4 - - + -
151A VAL 2.9 6.9 + - - +
152A PHE* 3.9 16.8 - - + -
153A LEU* 2.8 29.3 + - - +
181A ILE* 3.6 18.2 - - + +
182A ILE* 1.3 78.1 - - - +
184A ILE* 1.3 62.3 + - - +
201A ILE* 4.0 2.5 - - - -
203A VAL* 3.4 16.4 - - + +
205A ILE* 4.3 8.5 - - + -
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PHE* 4.8 0.9 - - - -
153A LEU* 3.2 21.1 - - + +
154A GLU* 4.2 0.2 - - - -
155A SER* 4.0 28.5 - - - +
166A VAL* 4.6 2.9 - - + -
183A MET* 1.3 75.4 - - - +
185A ASP* 1.3 72.2 + - - +
186A ASN* 3.3 9.6 + - + +
194A PHE* 3.9 26.2 - - + -
196A ALA* 3.7 27.1 - - + -
201A ILE* 3.8 21.3 - - + -
203A VAL 3.0 11.5 + - - +
204A SER* 4.0 4.7 - - - -
205A ILE* 2.8 32.8 + - - +
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 4.0 14.6 - - + +
111A TYR* 4.9 0.2 - - - +
114A SER* 4.7 2.9 + - - -
152A PHE* 4.1 16.4 - - + -
153A LEU 2.9 9.5 + - - -
154A GLU* 3.7 33.7 - - + +
155A SER 4.0 5.4 + - - +
156A PRO 5.3 0.2 - - - +
184A ILE* 1.3 77.0 - - - +
186A ASN* 1.3 56.1 + - - +
187A THR* 2.6 32.1 + - - -
188A TRP* 5.1 1.2 + - - +
205A ILE* 3.6 9.7 - - - +
207A ALA 5.5 0.7 - - - -
700A P3F 2.7 38.3 + - - +
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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