Contacts of the strand formed by residues 223 - 227 (chain A) in PDB entry 3COG
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 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ALA* 3.4 1.0 - - - -
87A PHE* 2.7 41.7 + - - -
89A SER 3.2 22.5 - - - -
90A GLY* 3.9 0.9 - - - -
93A ALA* 4.2 2.0 - - - -
208A TYR 3.4 9.4 - - - -
222A MET* 1.3 82.7 - - - +
224A LEU* 1.3 62.4 + - - +
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Residues in contact with LEU 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 LEU* 4.3 6.3 - - + -
72A GLU* 5.4 0.7 - - + -
75A VAL* 3.9 31.0 - - + -
84A CYS* 4.0 17.7 - - - -
85A LEU 3.4 2.9 - - - -
86A ALA* 3.8 22.0 - - + -
93A ALA* 4.4 1.0 - - - +
207A MET* 3.3 3.1 - - - +
208A TYR* 2.9 45.5 + - + +
210A ALA* 3.6 24.5 - - + -
214A MET* 4.0 18.6 - - + -
222A MET* 4.3 8.5 - - - -
223A GLY* 1.3 80.6 - - - +
225A VAL* 1.3 68.1 + - - +
226A SER 4.3 0.4 - - - -
255A CYS* 4.7 6.3 - - - -
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Residues in contact with VAL 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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84A CYS* 3.0 4.2 - - - -
85A LEU* 2.8 44.7 + - + +
87A PHE* 3.4 24.5 - - + -
93A ALA* 3.7 16.8 - - + -
97A ILE* 4.0 20.9 - - + -
205A ILE* 3.7 22.7 - - + -
206A SER 3.8 2.2 - - - -
207A MET* 4.4 2.2 - - + +
224A LEU* 1.3 80.9 - - - +
226A SER* 1.3 63.4 + - - +
236A LEU* 3.9 27.6 - - + -
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Residues in contact with SER 226 (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 VAL* 3.9 4.7 + - - +
76A ALA* 4.2 0.5 - - - -
79A ASP* 2.6 43.8 + - - +
81A ALA* 3.8 4.7 - - - -
83A TYR 3.3 8.0 + - - -
84A CYS* 3.7 18.9 - - - +
199A LEU* 4.0 5.9 - - - +
205A ILE* 3.4 8.1 - - - +
206A SER* 2.8 38.2 + - - -
208A TYR* 4.7 0.7 - - - -
225A VAL* 1.3 70.5 - - - +
227A VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 227 (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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81A ALA* 3.7 2.3 - - - +
82A LYS 3.5 2.6 + - - -
83A TYR* 2.9 45.8 + - + +
85A LEU* 4.2 11.9 - - + -
199A LEU* 4.3 1.8 - - - -
204A ASP 3.5 17.9 - - - +
205A ILE* 4.4 4.3 - - + -
225A VAL* 5.1 0.4 - - + +
226A SER* 1.3 75.3 - - - +
228A ASN* 1.3 64.8 + - - +
229A CYS 3.9 12.8 - - - +
232A LEU* 3.9 27.1 - - + -
233A HIS* 3.8 32.1 - - + +
236A LEU* 4.3 8.1 - - + -
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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