Contacts of the strand formed by residues 229 - 233 (chain A) in PDB entry 1G59
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 ARG 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 4.4 13.1 + - - -
2A VAL* 4.8 6.5 - - - +
28A TRP* 5.8 2.0 - - - -
159A LYS 5.7 0.2 - - - -
161A GLU* 3.8 19.7 - - + +
201A THR* 2.7 29.5 + - - +
202A ASP* 2.5 56.1 + - - +
203A VAL* 2.6 35.9 + - - +
228A PRO* 1.3 74.6 - - - +
230A PHE* 1.3 56.3 + - - +
231A TYR* 3.7 19.3 - - + -
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Residues in contact with PHE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 5.1 1.8 - - + -
159A LYS 4.1 17.5 + - - +
160A ASP* 3.5 4.3 - - - -
161A GLU* 2.7 36.5 + - - +
191A ASN* 5.5 2.2 - - - -
203A VAL* 3.3 43.1 - - + -
205A ARG* 4.3 18.8 - - - -
213A THR* 3.7 28.5 - - + -
216A HIS* 4.5 9.9 - - + -
217A VAL* 4.0 16.6 - - + -
220A TYR* 4.3 10.3 - + - -
227A ALA* 5.0 2.9 - - + -
228A PRO* 3.7 33.4 + - + -
229A ARG* 1.3 73.5 - - - +
231A TYR* 1.3 61.4 + - - +
232A HIS* 4.3 13.0 - - + +
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Residues in contact with TYR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TRP* 3.6 17.7 - - - -
160A ASP* 4.4 1.3 - - - -
161A GLU* 3.3 27.8 - - + +
162A LEU* 3.6 20.2 - - + -
202A ASP* 3.3 31.1 + - + -
203A VAL 2.8 9.6 + - - +
204A ILE* 3.3 26.8 - - + +
205A ARG 2.9 25.6 + - - +
229A ARG* 3.7 22.5 - - + -
230A PHE* 1.3 76.7 - - - +
232A HIS* 1.3 63.9 + - - +
233A MET 3.9 0.4 + - - -
295A TRP* 3.2 49.8 - + + -
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Residues in contact with HIS 232 (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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160A ASP* 2.8 34.5 + - + +
162A LEU* 4.1 7.7 - - - +
163A ARG* 2.2 39.8 + - - +
205A ARG* 2.9 46.7 - - - +
206A ALA 3.5 6.7 + - - -
207A GLU* 3.7 12.1 - - - -
209A TRP 3.8 0.9 - - - -
210A LEU* 3.7 33.3 + - + +
213A THR* 3.2 25.0 + - - +
230A PHE* 4.3 13.9 - - + +
231A TYR* 1.3 73.7 - - - +
233A MET* 1.3 62.7 + - - +
234A PRO* 4.1 0.5 - - - +
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Residues in contact with MET 233 (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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20A TYR* 3.6 25.4 - - + +
21A ILE* 3.5 32.1 - - + -
24A PHE* 3.4 45.1 - - + -
162A LEU* 4.9 1.3 - - - -
204A ILE* 4.1 16.2 - - + -
205A ARG 2.6 8.1 + - - -
206A ALA* 3.4 1.2 - - - -
207A GLU* 2.5 31.4 + - - +
231A TYR 3.9 0.4 + - - -
232A HIS* 1.3 75.8 - - - +
234A PRO* 1.3 66.8 - - + +
273A MET 4.7 2.0 - - - +
274A GLY* 5.4 1.1 - - - -
295A TRP* 3.8 24.9 - - + -
298A VAL* 4.1 19.1 - - + -
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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