Contacts of the strand formed by residues 235 - 241 (chain G) in PDB entry 6S1M
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 235 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144G PHE* 5.9 0.2 - - + -
160G ILE* 4.2 8.7 - - + -
207G PHE* 3.1 42.5 - - + -
212G LEU* 3.8 28.0 - - + -
227G LEU* 4.3 11.0 - - + -
228G SER 3.7 7.9 - - - +
229G MET* 3.6 31.0 - - + +
233G VAL 3.5 2.6 + - - -
234G PRO* 1.3 74.6 - - - +
236G VAL* 1.3 76.0 + - - +
237G VAL* 3.8 15.2 - - + +
249G TYR 3.5 1.0 - - - +
250G TYR* 3.3 5.5 - - - -
251G LEU* 2.9 33.4 + - + +
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Residues in contact with VAL 236 (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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133G TYR* 3.1 41.5 - - + +
226G THR 3.6 1.6 - - - +
227G LEU* 3.3 6.4 - - - -
228G SER* 2.8 47.5 + - - +
234G PRO 4.0 1.1 - - - +
235G LEU* 1.3 77.1 - - - +
237G VAL* 1.3 69.5 + - - +
238G GLU* 4.0 6.3 - - + +
248G LYS* 4.6 16.2 - - + -
249G TYR 3.6 4.0 - - - +
250G TYR* 3.6 31.2 - - + +
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Residues in contact with VAL 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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144G PHE* 4.1 10.5 - - + -
212G LEU* 4.5 4.7 - - + -
215G PHE* 3.9 24.0 - - + -
225G VAL* 3.9 11.0 - - + -
226G THR 3.8 2.9 - - - -
227G LEU* 3.8 19.1 - - + -
235G LEU* 3.8 21.5 - - + -
236G VAL* 1.3 77.4 - - - +
238G GLU* 1.3 60.7 + - - +
239G TYR* 3.7 24.5 - - + +
248G LYS* 3.5 0.9 - - - -
249G TYR* 2.7 52.2 + - + +
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Residues in contact with GLU 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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224G THR 4.6 0.2 - - - +
225G VAL* 3.2 5.9 - - - +
226G THR* 3.2 50.2 + - + +
236G VAL* 4.0 7.5 - - + +
237G VAL* 1.3 76.6 - - - +
239G TYR* 1.3 73.3 + - - +
240G LYS* 3.4 34.5 + - + +
246G HIS* 3.5 7.3 - - + -
247G LEU 3.5 4.0 - - - +
248G LYS* 3.0 43.1 - - + -
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Residues in contact with TYR 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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141G SER* 4.0 16.4 + - - -
144G PHE* 3.8 19.6 - - - -
215G PHE 3.5 19.6 + - - -
216G THR* 3.5 22.3 + - - +
218G ALA* 3.7 27.6 - - + +
219G THR* 4.0 13.4 + - - -
221G LEU* 4.8 5.2 - - + -
222G SER* 4.5 9.4 - - - -
224G THR 4.2 9.0 - - - -
225G VAL* 3.6 25.8 - - + -
237G VAL* 3.7 19.1 - - + -
238G GLU* 1.3 77.3 - - - +
240G LYS* 1.3 64.6 + - - +
241G ILE* 4.2 0.7 - - - +
246G HIS* 3.4 1.9 - - - +
247G LEU* 2.9 39.8 + - + +
249G TYR* 3.9 14.6 - + - -
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Residues in contact with LYS 240 (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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53G ARG* 4.7 10.3 - - - +
221G LEU 3.4 6.8 - - - +
222G SER* 3.3 30.0 + - - +
224G THR 4.7 1.2 + - - -
226G THR* 6.1 5.8 - - + -
238G GLU* 3.4 30.1 + - + +
239G TYR* 1.3 74.9 - - - +
241G ILE* 1.3 61.1 + - - +
242G ALA* 3.6 6.5 + - - +
245G GLY 4.0 4.9 - - - +
246G HIS* 4.0 22.0 + - + -
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Residues in contact with ILE 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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11G ILE* 4.0 26.9 - - + -
15G VAL* 4.2 13.5 - - + -
50G LEU* 3.8 17.7 - - + -
52G LEU* 4.0 11.0 - - + -
221G LEU* 4.2 30.1 - - + +
239G TYR 4.2 2.2 - - - +
240G LYS* 1.3 74.6 - - - +
242G ALA* 1.3 67.5 + - - +
243G ASP 3.8 0.4 - - - -
244G MET* 2.7 34.1 + - + +
245G GLY 2.8 18.8 + - - +
246G HIS* 3.7 29.2 - - - +
247G LEU* 4.3 1.1 - - + +
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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