Contacts of the strand formed by residues 223 - 227 (chain D) in PDB entry 5B2G
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 LEU 223 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C PHE* 3.5 51.6 - - + -
40C ILE* 4.5 5.4 - - + -
41C VAL 5.4 1.8 - - - +
44C GLN* 3.5 22.2 - - - +
46C ILE* 3.5 18.4 - - + -
215D LEU* 4.3 8.5 - - - +
218D ASN* 3.3 27.1 - - - +
221D GLY 3.8 0.6 - - - -
222D ASN* 1.3 82.7 + - - +
224D TYR* 1.3 72.1 + - - +
225D ASP 4.6 0.7 - - - +
315D LEU* 4.0 14.8 - - + -
316D PHE 3.4 7.4 - - - +
317D GLN* 3.6 22.9 - - - +
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Residues in contact with TYR 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 6.0 0.2 - - - -
48C GLU* 5.4 8.1 - - - -
72C ALA* 4.6 17.5 + - + +
73C LEU 5.2 0.5 + - - -
74C PRO* 5.3 6.4 - - - +
209D LEU* 4.5 6.5 - - + +
214D ALA* 3.2 49.8 - - + +
215D LEU* 4.2 11.7 - - + -
217D SER* 3.9 10.3 - - - -
218D ASN* 5.1 3.4 - - + -
223D LEU* 1.3 81.7 - - - +
225D ASP* 1.3 69.1 + - - +
226D TRP* 3.7 39.1 + + + -
315D LEU* 3.4 4.5 - - - +
316D PHE* 2.9 40.6 + + + +
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Residues in contact with ASP 225 (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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33C THR* 4.8 1.9 - - + +
35C PHE* 3.8 25.5 - - + -
48C GLU* 6.1 0.7 - - - +
156C GLN* 2.5 37.6 + - - +
158C ARG* 3.6 23.3 + - - +
223D LEU* 4.6 1.6 - - - +
224D TYR* 1.3 84.3 + - - +
226D TRP* 1.3 61.2 + - - +
227D ARG* 2.4 30.7 + - - +
313D SER* 3.4 9.2 + - - -
314D ILE 3.8 5.2 - - - +
315D LEU* 4.1 2.9 - - + +
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Residues in contact with TRP 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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207D GLU* 3.7 20.8 + - - -
208D ARG 5.9 0.4 + - - -
209D LEU* 3.6 28.6 - - + +
224D TYR* 3.7 22.5 + + + -
225D ASP* 1.3 73.3 - - - +
227D ARG* 1.3 74.5 + - - +
228D SER* 3.9 12.6 - - - -
238D LEU* 3.7 25.6 - - + -
240D LEU* 3.5 37.7 - - + +
300D MSE 3.8 24.0 - - + -
312D TYR* 4.5 5.6 - - + -
313D SER* 3.2 9.5 + - - -
314D ILE* 3.0 57.1 + - + +
316D PHE* 4.0 12.8 - + + -
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Residues in contact with ARG 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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142C ASN 6.0 0.7 - - - -
146C ASP* 2.6 41.4 + - - -
152C VAL* 3.4 17.4 - - - +
156C GLN* 3.3 18.8 + - - +
158C ARG* 2.8 46.6 - - - +
225D ASP* 2.4 38.0 + - - +
226D TRP* 1.3 84.7 + - - +
228D SER* 1.3 69.8 + - - +
229D SER* 5.2 0.5 + - - -
311D PRO* 5.1 8.5 - - + -
312D TYR 3.4 11.7 - - - +
313D SER* 3.3 18.7 + - - +
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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