Contacts of the strand formed by residues 236 - 242 (chain G) in PDB entry 1R8Y
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 SER 236 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25G GLU* 3.1 29.0 - - - +
29G VAL* 3.2 34.1 - - - +
220G TYR 3.9 0.3 - - - +
221G THR* 3.5 1.7 - - - -
222G VAL* 2.8 40.1 + - - +
224G VAL* 4.7 11.1 - - - +
234G GLY 4.1 0.8 - - - -
235G PHE* 1.3 75.8 + - - +
237G LYS* 1.3 62.1 + - - +
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Residues in contact with LYS 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G GLU* 3.7 13.7 + - - +
26G ALA* 3.7 18.7 - - - +
29G VAL* 4.3 1.9 - - - +
219G ASP* 5.3 13.6 - - + +
220G TYR 3.1 11.9 - - - +
221G THR* 3.6 28.9 + - + +
235G PHE* 5.2 3.1 - - + +
236G SER* 1.3 76.7 - - - +
238G PHE* 1.3 64.8 + - - +
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Residues in contact with PHE 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ALA* 3.9 19.1 - - + +
29G VAL* 4.1 11.2 - - + -
30G TRP* 3.9 34.3 - + + -
33G TYR* 3.5 37.5 - + + -
219G ASP* 3.4 3.0 - - - +
220G TYR* 2.7 78.8 + + + +
222G VAL* 4.4 11.2 - - + -
237G LYS* 1.3 74.6 - - - +
239G ARG* 1.3 60.3 + - - +
240G LEU* 3.8 25.4 - - + -
9H SER* 3.5 11.4 - - - +
12H VAL* 4.5 1.1 - - + -
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Residues in contact with ARG 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205G SER* 4.8 5.7 + - - -
217G THR* 3.6 24.2 - - + +
218G LEU 3.3 5.2 - - - +
219G ASP* 2.8 41.2 + - - +
220G TYR* 4.9 0.2 - - - -
238G PHE* 1.3 75.7 - - - +
240G LEU* 1.3 73.4 + - - +
5H TYR* 3.4 32.9 - - - +
6H ARG* 2.9 42.9 + - - +
7H THR 4.2 5.8 - - - +
8H ARG* 3.5 4.7 - - - +
9H SER* 2.4 43.3 + - - +
12H VAL* 3.9 0.3 - - - +
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Residues in contact with LEU 240 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30G TRP* 4.3 6.7 - - + +
33G TYR* 4.0 17.7 - - + -
142G HIS* 6.1 1.6 - - - +
217G THR* 3.5 1.2 - - - +
218G LEU* 2.9 30.7 + - - -
220G TYR* 4.0 6.9 - - + -
238G PHE* 3.8 25.1 - - + -
239G ARG* 1.3 74.8 - - - +
241G SER* 1.3 65.6 + - - +
242G TYR* 3.6 31.5 - - + +
7H THR 3.9 1.3 - - - -
8H ARG* 4.3 8.3 - - + -
12H VAL* 3.3 35.9 - - + -
13H ALA 4.4 10.5 - - - +
14H ALA* 5.7 4.5 - - + -
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Residues in contact with SER 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G ALA 4.4 2.1 - - - +
142G HIS* 4.5 12.3 - - - +
215G MET* 3.7 16.1 - - - -
216G VAL 3.4 4.3 - - - -
217G THR* 2.6 31.5 + - - +
240G LEU* 1.3 73.9 - - - +
242G TYR* 1.3 72.9 + - - +
7H THR* 2.4 36.1 + - - -
8H ARG* 4.7 2.8 - - - +
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Residues in contact with TYR 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G TYR* 4.1 4.9 + - - -
138G ASN* 4.1 12.6 - - + -
141G ALA* 3.3 10.3 - - + +
142G HIS* 3.7 31.8 + + - -
175G ARG* 6.1 2.0 - - - -
177G TYR* 3.1 32.5 - - + +
215G MET* 3.5 8.6 - - - +
216G VAL* 2.7 42.9 + - + +
218G LEU* 3.8 26.7 - - + -
220G TYR* 2.9 20.6 + - - -
240G LEU* 3.6 35.5 - - + +
241G SER* 1.3 82.0 - - - +
243G TYR* 1.3 60.4 + - - +
244G PRO* 3.6 0.4 - - - +
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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