Contacts of the strand formed by residues 242 - 250 (chain G) in PDB entry 1DE4
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 TYR 242 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33G ASP 4.9 4.9 + - - -
207G ASN* 3.3 8.0 + - - -
208G TYR* 2.9 55.0 + - + +
209G TYR* 4.5 11.1 - + - -
210G PRO 4.3 6.1 - - - -
211G GLN* 3.3 49.8 + - + -
234G VAL* 4.2 9.6 - - + -
235G LEU 3.2 19.7 - - - +
236G PRO* 3.8 22.2 - - + -
237G ASN* 3.7 4.3 - - - +
240G GLY* 3.5 26.9 + - - -
241G THR* 1.3 74.3 - - - +
243G GLN* 1.3 61.7 + - - +
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Residues in contact with GLN 243 (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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204G ARG* 2.8 33.2 + - + +
205G ALA 3.1 13.9 - - - +
206G LEU* 3.6 16.4 - - + +
207G ASN 4.5 0.2 - - - +
208G TYR* 3.4 5.4 - - - -
233G ASP 3.8 0.2 - - - +
235G LEU* 2.8 40.3 + - + +
237G ASN* 3.2 27.8 + - - +
242G TYR* 1.3 78.8 - - - +
244G GLY* 1.3 59.4 + - - +
245G TRP* 4.1 7.7 - - + -
10H TYR* 3.3 19.9 - - + -
11H SER 3.1 19.2 + - - -
12H ARG* 3.9 4.8 + - - +
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Residues in contact with GLY 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G ARG* 3.5 0.8 - - - -
205G ALA* 2.8 31.8 + - - +
208G TYR* 3.8 8.4 - - - -
215G MET* 3.1 20.5 - - - +
233G ASP 3.4 14.1 - - - -
234G VAL* 4.2 3.8 - - - -
235G LEU* 5.6 0.2 - - - -
243G GLN* 1.3 75.8 - - - +
245G TRP* 1.3 62.7 + - - +
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Residues in contact with TRP 245 (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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202G ARG* 4.3 11.7 - - + -
203G CYS 3.2 13.0 - - - +
204G ARG* 3.3 55.6 - - + -
215G MET* 3.2 1.9 - - - +
231G PRO 4.7 1.0 - - - +
233G ASP* 3.3 45.6 + - + +
235G LEU* 4.1 20.2 - - + -
243G GLN* 4.1 9.0 - - + -
244G GLY* 1.3 78.2 - - - +
246G ILE* 1.3 67.8 + - - +
247G THR* 5.2 2.2 - - - -
8H GLN* 5.3 3.8 - - + -
9H VAL 4.9 1.8 - - - -
10H TYR* 3.6 25.8 - + + -
99H MET* 3.8 44.9 - - + +
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Residues in contact with ILE 246 (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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202G ARG* 3.7 1.1 - - - -
203G CYS* 3.1 24.0 + - + +
215G MET* 3.6 45.1 - - + +
216G LYS* 3.7 11.0 - - - +
217G TRP* 3.0 48.6 - - + +
229G PHE* 5.0 2.9 - - + -
230G GLU 4.4 11.2 - - - +
231G PRO 5.6 0.2 - - - -
232G LYS* 3.6 26.5 - - - +
245G TRP* 1.3 83.1 - - - +
247G THR* 1.3 62.0 + - - +
260G CYS* 4.0 9.6 - - - -
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Residues in contact with THR 247 (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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200G THR* 3.3 29.7 - - + +
201G LEU 3.2 5.7 + - - -
202G ARG* 4.5 8.3 - - - +
217G TRP* 3.3 10.2 + - - -
229G PHE* 3.5 17.5 - - - +
230G GLU* 3.9 28.0 + - - +
245G TRP* 5.2 3.0 - - - -
246G ILE* 1.3 73.6 + - - +
248G LEU* 1.3 68.3 + - - +
249G ALA* 4.7 1.3 - - + +
99H MET* 4.0 21.3 - - - +
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Residues in contact with LEU 248 (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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199G THR 3.8 1.0 - - - +
200G THR* 3.5 0.6 - - - -
201G LEU* 2.7 39.4 + - + +
217G TRP* 3.4 41.1 - - + +
224G MET* 3.9 20.4 - - + -
228G GLU* 4.0 30.7 - - + +
247G THR* 1.3 83.2 - - - +
249G ALA* 1.3 66.7 + - - +
250G VAL* 3.7 15.2 + - + -
258G TYR* 3.7 33.2 - - + -
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Residues in contact with ALA 249 (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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138A PRO* 5.7 7.6 - - + -
141A TRP* 3.9 33.7 - - + +
198G VAL* 4.2 11.2 - - + -
199G THR 3.7 4.9 - - - -
200G THR* 4.4 9.0 - - + +
228G GLU* 5.5 1.6 - - - +
247G THR* 4.7 2.1 - - + +
248G LEU* 1.3 78.5 - - - +
250G VAL* 1.3 68.6 + - - +
251G PRO* 4.8 0.3 - - - +
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Residues in contact with VAL 250 (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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141A TRP* 3.9 0.9 - - - -
198G VAL* 2.8 26.1 - - - +
199G THR* 2.9 23.5 + - - +
201G LEU* 4.2 18.6 - - + -
248G LEU* 3.7 18.4 - - + +
249G ALA* 1.3 80.6 - - - +
251G PRO* 1.3 73.8 - - + +
254G GLU* 4.8 0.4 - - + -
255G GLU* 4.1 21.1 - - - +
258G TYR* 3.2 42.0 - - + +
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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