Contacts of the strand formed by residues 203 - 207 (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 VAL 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A SER* 4.6 1.6 - - - +
97A PHE* 4.6 0.4 - - + -
181A ILE* 4.1 21.5 - - + -
182A ILE 3.2 3.2 + - - -
183A MET* 3.4 12.5 - - + -
184A ILE 3.0 25.6 + - - +
197A LEU* 4.2 0.2 - - - -
201A ILE* 3.4 6.3 - - - +
202A ASP* 1.3 84.4 - - + +
204A SER* 1.3 61.4 + - - +
205A ILE* 3.8 23.6 - - + -
223A ALA* 4.0 9.0 - - + -
224A VAL 3.4 9.4 - - - +
225A CYS* 4.2 7.0 - - - -
229A CYS* 4.4 7.9 - - + -
233A LEU* 3.7 33.4 - - + -
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Residues in contact with SER 204 (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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75A GLU* 2.6 31.4 + - - +
184A ILE* 3.9 5.4 - - - -
186A ASN* 3.3 23.4 + - - +
196A ALA* 4.0 11.2 - - - -
197A LEU* 3.7 19.2 - - - +
203A VAL* 1.3 73.0 - - - +
205A ILE* 1.3 59.9 + - - +
206A GLN* 4.2 0.5 + - - +
222A THR* 3.9 1.2 + - - +
223A ALA* 3.5 0.7 - - - -
224A VAL* 2.8 40.1 + - - +
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Residues in contact with ILE 205 (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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86A GLY 4.6 0.7 - - - +
89A ALA* 3.7 20.9 - - + -
90A VAL* 3.8 23.3 - - + -
93A SER* 3.9 26.9 - - - +
152A PHE* 3.8 28.0 - - + -
183A MET* 4.3 12.6 - - + -
184A ILE 2.8 15.9 + - - +
185A ASP* 3.6 6.5 - - - -
186A ASN* 2.8 31.0 + - - -
203A VAL* 3.8 14.8 - - + +
204A SER* 1.3 75.7 - - - +
206A GLN* 1.3 70.8 + - - +
207A ALA 5.1 0.2 - - - +
222A THR 3.3 11.0 - - - +
223A ALA* 4.4 1.6 - - + -
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Residues in contact with GLN 206 (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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71A MET* 3.8 3.0 - - - +
75A GLU* 2.8 29.3 + - - +
86A GLY* 4.0 2.4 - - - -
186A ASN* 3.9 14.4 - - + +
187A THR* 3.4 9.2 - - - +
190A ALA* 3.2 24.0 + - - -
191A GLY* 3.2 25.0 - - - +
204A SER 5.2 0.2 - - - +
205A ILE* 1.3 84.6 - - - +
207A ALA* 1.3 62.6 + - - +
208A ALA* 3.2 8.2 + - - +
211A TYR 5.9 0.3 + - - -
212A LEU* 3.5 27.8 + - - +
221A GLY* 3.2 5.4 - - - -
222A THR* 3.0 41.8 + - - +
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Residues in contact with ALA 207 (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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86A GLY* 3.6 14.5 - - - -
185A ASP* 4.8 0.4 + - - -
187A THR* 2.8 17.1 + - + +
206A GLN* 1.3 72.3 - - - +
208A ALA* 1.3 55.5 + - - +
209A THR 3.0 5.2 - - - -
210A LYS* 3.0 36.0 + - + +
211A TYR 4.7 0.2 + - - -
212A LEU 5.4 0.2 + - - -
220A ILE 3.9 0.7 - - - -
700A P3F 3.2 47.7 - - + +
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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