Contacts of the strand formed by residues 221 - 225 (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 GLY 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A LEU* 3.6 1.9 - - - -
83A PHE* 2.9 37.5 + - - +
85A CYS 3.3 22.3 - - - -
86A GLY* 3.7 1.1 - - - -
89A ALA* 4.0 3.1 - - - -
206A GLN 3.2 10.8 - - - -
220A ILE* 1.3 76.1 - - - +
222A THR* 1.3 68.9 + - - +
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Residues in contact with THR 222 (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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67A LEU* 5.1 2.0 - - + -
71A MET* 4.1 24.8 - - + +
75A GLU* 4.7 1.4 + - - -
80A CYS* 4.1 12.8 - - - -
81A VAL 3.4 5.4 - - - -
82A LEU* 3.9 19.1 - - + -
89A ALA* 4.0 2.8 - - - +
204A SER 4.4 0.7 + - - -
205A ILE* 3.3 7.2 - - - +
206A GLN* 3.0 49.6 + - - +
208A ALA* 4.1 16.7 - - + +
220A ILE* 4.5 6.1 - - + -
221A GLY* 1.3 79.7 - - - +
223A ALA* 1.3 62.2 + - - +
224A VAL* 4.1 1.2 - - - +
252A THR* 5.6 0.4 - - + -
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Residues in contact with ALA 223 (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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80A CYS* 3.4 0.9 - - - -
81A VAL* 2.9 33.3 + - + +
83A PHE* 3.7 15.5 - - + -
89A ALA* 5.0 0.4 - - + -
93A SER* 3.6 22.9 - - - +
203A VAL* 4.0 14.1 - - + -
204A SER 3.5 6.1 - - - -
205A ILE* 4.3 3.1 - - + +
222A THR* 1.3 76.7 - - - +
224A VAL* 1.3 63.0 + - - +
225A CYS* 3.8 5.6 + - - -
233A LEU* 4.3 7.2 - - + -
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Residues in contact with VAL 224 (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 35.2 - - + +
72A CYS* 4.5 2.9 - - - -
75A GLU* 3.6 35.9 - - + +
77A GLY* 3.7 25.8 - - - +
79A GLY 3.4 10.8 - - - +
80A CYS* 4.1 7.6 - - + -
197A LEU* 3.8 13.3 - - + +
203A VAL* 3.4 1.7 - - - -
204A SER* 2.8 42.6 + - - +
222A THR* 5.2 1.3 - - - +
223A ALA* 1.3 73.4 - - - +
225A CYS* 1.3 61.8 + - - +
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Residues in contact with CYS 225 (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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77A GLY* 3.5 1.9 - - - -
78A ALA 2.9 24.1 + - - -
79A GLY 2.9 11.4 + - - +
81A VAL* 4.4 7.2 - - - -
197A LEU* 4.0 3.8 - - - -
202A ASP 3.5 7.0 - - - +
203A VAL* 4.2 7.2 - - - +
223A ALA 3.8 10.3 - - - -
224A VAL* 1.3 77.0 - - - +
226A ASN* 1.3 69.5 + - - +
229A CYS* 4.2 2.9 - - + -
230A TRP* 3.6 22.7 - - + +
233A LEU* 3.5 43.3 - - - -
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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