Contacts of the strand formed by residues 235 - 241 (chain G) in PDB entry 4GEK
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 PHE 235 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35G SER 3.9 4.7 - - - -
36G VAL* 3.8 29.4 - - + -
37G PRO* 3.5 30.5 - - + +
42G ILE* 5.9 0.4 - - + -
133G PHE* 3.9 15.0 - + + -
136G GLN* 5.9 1.3 - - - -
164G GLU 3.6 3.6 - - - +
165G LYS* 3.6 37.7 - - + -
166G PHE* 3.9 4.9 - - - -
181G HIS* 3.5 37.0 - + - -
199G ARG* 5.5 3.1 - - - -
203G GLU* 4.2 4.9 - - - -
230G PHE* 4.8 0.6 - - - -
231G GLN* 3.3 5.4 - - - +
232G CYS 2.8 31.4 + - - +
233G PHE 3.3 0.2 - - - -
234G ASN* 1.3 103.7 - - - +
236G GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 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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42G ILE* 4.5 3.8 - - - -
133G PHE* 4.3 2.2 - - - -
163G SER* 3.2 4.9 - - - -
164G GLU 2.9 32.5 + - - -
166G PHE* 3.4 16.5 - - - -
230G PHE* 3.2 18.8 - - - -
231G GLN* 3.9 1.8 - - - -
235G PHE* 1.3 77.7 - - - +
237G SER* 1.3 61.6 + - - -
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Residues in contact with SER 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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42G ILE* 4.3 9.7 - - - +
161G VAL* 3.3 10.4 - - - +
162G LEU 3.4 4.9 + - - -
163G SER* 2.7 26.1 + - - -
166G PHE* 3.9 2.0 - - - -
228G LEU* 3.4 4.1 - - - +
229G TRP* 2.9 53.0 + - - -
230G PHE* 2.8 21.3 + - - +
236G GLY* 1.3 75.8 - - - -
238G LEU* 1.3 65.2 + - - +
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Residues in contact with LEU 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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160G LEU 3.7 0.5 - - - +
161G VAL* 3.4 4.9 - - - +
162G LEU* 2.7 52.4 + - + +
166G PHE* 3.8 31.4 - - + -
211G VAL* 4.4 6.5 - - + -
214G HIS* 4.1 18.8 - - + -
215G LYS* 3.8 32.5 - - + -
218G LEU* 4.3 24.2 - - + -
227G GLU 3.2 9.2 - - - +
228G LEU* 4.0 18.8 - - + +
229G TRP* 4.0 2.7 - - - -
237G SER* 1.3 75.8 + - - +
239G VAL* 1.3 59.3 + - - +
240G ALA* 5.7 0.2 - - - -
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Residues in contact with VAL 239 (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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173A VAL* 5.8 3.5 - - + +
176A LEU* 3.9 31.9 - - + -
177A LEU* 5.2 2.2 - - + -
49G LEU* 4.1 24.2 - - + -
159G ALA* 4.6 0.9 - - + -
160G LEU 3.3 9.2 - - - +
161G VAL* 4.8 0.4 - - + -
225G HIS 4.6 0.2 - - - -
226G SER* 3.2 3.3 - - - -
227G GLU* 2.9 46.4 + - + +
229G TRP* 4.0 31.1 - - + -
238G LEU* 1.3 74.5 - - - +
240G ALA* 1.3 64.3 + - - +
241G LEU* 4.2 13.8 - - + +
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Residues in contact with ALA 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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159G ALA* 3.3 4.3 - - - +
160G LEU* 2.8 37.5 + - + +
218G LEU* 4.0 20.2 - - + -
223G PHE* 3.5 28.5 - - + -
225G HIS 3.2 4.9 - - - -
226G SER* 3.6 15.0 - - - +
238G LEU 4.2 0.4 - - - -
239G VAL* 1.3 75.8 - - - +
241G LEU* 1.3 62.3 + - - +
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Residues in contact with LEU 241 (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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172A LYS* 4.0 37.0 - - + +
173A VAL* 4.9 4.7 - - + -
176A LEU* 4.2 20.4 - - + -
53G PHE* 3.7 34.1 - - + -
157G GLY 5.7 0.4 - - - +
158G GLY 3.6 1.8 - - - +
159G ALA* 3.9 15.3 - - + -
223G PHE* 3.5 6.1 - - - -
224G GLU* 3.5 8.1 + - - +
225G HIS* 2.8 45.8 + - + +
239G VAL* 4.2 13.7 - - + +
240G ALA* 1.3 77.2 - - - +
242G LYS* 1.3 65.3 + - - +
243G ALA 3.9 0.2 + - - -
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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