Contacts of the strand formed by residues 223 - 227 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D ALA* 3.5 1.2 - - - -
87D PHE* 2.8 39.4 + - - +
89D SER 3.2 20.7 - - - -
90D GLY* 3.6 1.3 - - - -
93D ALA* 4.4 1.8 - - - -
208D TYR 3.2 11.7 - - - -
210D ALA 4.2 0.2 - - - -
222D MET* 1.3 79.8 - - - +
224D LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D LEU* 4.2 9.6 - - + -
72D GLU* 5.6 0.4 - - + -
75D VAL* 3.9 21.5 - - + -
84D CYS* 4.3 11.4 - - - -
85D LEU 3.4 3.1 - - - -
86D ALA* 3.9 21.3 - - + -
93D ALA* 4.5 0.8 - - - +
207D MET* 3.3 4.4 - - - +
208D TYR* 2.8 43.4 + - + +
210D ALA* 3.7 22.9 - - + -
214D MET* 3.8 32.3 - - + -
222D MET* 4.2 10.5 - - - -
223D GLY* 1.3 83.0 - - - +
225D VAL* 1.3 66.5 + - - +
226D SER 4.3 0.4 - - - -
255D CYS* 4.6 5.2 - - - -
259D LEU* 5.6 0.2 - - + -
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Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D CYS* 3.2 2.8 - - - -
85D LEU* 2.8 41.3 + - + +
87D PHE* 3.5 27.8 - - + -
93D ALA* 3.7 17.5 - - + -
97D ILE* 4.0 20.0 - - + -
205D ILE* 3.5 24.9 - - + -
206D SER 3.6 3.4 - - - -
207D MET* 4.4 2.5 - - + -
224D LEU* 1.3 80.7 - - - +
226D SER* 1.3 61.7 + - - +
236D LEU* 4.0 26.9 - - + -
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Residues in contact with SER 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D VAL* 3.9 3.8 + - - +
76D ALA* 4.1 0.5 - - - -
79D ASP* 2.7 44.0 + - - +
81D ALA* 3.8 4.3 - - - -
83D TYR 3.3 9.0 - - - -
84D CYS* 3.6 20.6 - - - +
199D LEU* 3.9 6.1 - - - +
205D ILE* 3.4 8.1 - - - +
206D SER* 2.8 34.3 + - - -
208D TYR* 5.0 0.3 - - - -
225D VAL* 1.3 70.8 - - - +
227D VAL* 1.3 61.8 + - - +
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Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ALA* 3.8 2.5 - - - +
82D LYS 3.5 2.6 + - - -
83D TYR* 2.9 44.1 + - + +
85D LEU* 4.2 6.5 - - + -
199D LEU* 4.2 2.7 - - - -
204D ASP 3.4 19.1 - - - +
205D ILE* 4.3 1.8 - - + -
226D SER* 1.3 76.6 - - - +
228D ASN* 1.3 65.8 + - - +
229D CYS 4.0 9.0 - - - +
232D LEU* 3.7 31.0 - - + -
233D HIS* 3.9 30.5 - - + -
236D LEU* 4.1 17.3 - - + -
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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