Contacts of the strand formed by residues 234 - 241 (chain I) in PDB entry 3Q3G
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 234 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I ASP* 3.3 29.0 + - + +
133I SER* 3.9 9.3 - - - +
134I ASP* 2.8 33.6 + - - +
232I ASN 5.7 1.6 - - - -
233I ALA* 1.3 71.6 - - - +
235I LYS* 1.3 60.9 + - - +
236I ILE* 3.6 12.3 + - + +
265I ILE* 4.1 18.4 - - + -
319I ILE* 3.6 38.1 - - + -
320I GLU 3.5 26.0 - - - -
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Residues in contact with LYS 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I ASP* 3.8 8.3 - - + +
223I PHE* 4.1 39.5 + - + +
229I ALA* 6.0 2.7 - - - -
230I ARG 4.6 14.4 - - - +
231I LYS* 4.9 9.4 + - - +
233I ALA 3.5 8.9 + - - +
234I PHE* 1.3 69.8 - - - +
236I ILE* 1.3 55.2 + - - +
262I GLU* 3.3 44.9 + - - +
263I GLY 3.5 14.9 + - - +
264I VAL* 3.4 17.6 - - + -
265I ILE* 2.7 40.0 + - - +
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Residues in contact with ILE 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I SER* 4.4 10.3 - - - +
134I ASP 3.0 10.4 + - - +
135I ILE* 3.9 24.9 - - + -
136I ALA 2.8 29.3 + - - -
223I PHE* 3.3 7.2 - - - -
234I PHE* 4.3 19.1 - - + +
235I LYS* 1.3 78.2 - - - +
237I LEU* 1.3 61.2 + - - +
238I VAL* 4.7 0.2 - - + -
264I VAL* 4.6 0.2 - - - -
265I ILE* 3.3 20.6 - - + +
267I TYR* 3.8 27.4 - - + -
316I ILE* 3.8 40.8 - - + +
319I ILE 5.5 3.8 - - - +
320I GLU 6.5 0.2 - - - -
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Residues in contact with LEU 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I ALA* 3.4 19.5 - - + +
137I PHE 4.3 0.4 - - - -
138I LEU* 3.8 24.2 - - + +
215I ILE* 4.5 17.9 - - + -
218I VAL* 3.6 32.1 - - + -
219I VAL* 5.6 1.3 - - + -
223I PHE* 4.6 2.2 - - + -
236I ILE* 1.3 76.5 - - - +
238I VAL* 1.3 60.3 + - - +
239I VAL* 3.6 20.0 - - + -
264I VAL* 3.8 18.8 - - + -
265I ILE 2.7 10.6 + - - +
266I ARG* 3.5 16.9 - - + -
267I TYR* 2.7 34.7 + - - +
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Residues in contact with VAL 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I ILE* 4.1 22.0 - - + -
136I ALA 2.8 9.0 + - - +
137I PHE* 3.5 25.9 - - + -
138I LEU 2.9 23.4 + - - -
156I PHE* 5.3 0.7 - - + -
160I VAL* 5.8 0.9 - - + -
236I ILE* 4.7 1.1 - - + -
237I LEU* 1.3 73.9 - - - +
239I VAL* 1.3 60.8 + - - +
240I ILE* 3.5 22.6 - - + +
267I TYR* 3.6 9.4 - - + +
269I ILE* 4.0 21.1 - - + -
312I LEU* 4.3 18.2 - - + -
316I ILE* 4.5 17.0 - - + -
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Residues in contact with VAL 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I LEU* 3.4 31.0 - - + +
176I TYR* 4.8 4.0 - - + +
211I THR* 4.6 13.2 - - + -
215I ILE* 4.7 1.8 - - + -
237I LEU* 3.6 33.2 - - + -
238I VAL* 1.3 70.3 - - - +
240I ILE* 1.3 63.4 + - - +
241I THR* 4.9 2.5 - - - -
266I ARG* 5.6 1.8 - - + -
267I TYR 2.8 16.3 + - - +
268I VAL* 3.3 14.9 - - + +
269I ILE* 2.8 32.1 + - - +
287I ILE* 4.1 23.3 - - + -
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Residues in contact with ILE 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I PHE* 4.0 10.8 - - + -
138I LEU 2.9 9.4 + - - +
139I ILE* 3.6 23.3 - - + -
140I ASP* 2.8 32.1 + - - +
153I MET* 3.8 29.4 - - + -
156I PHE* 4.8 6.5 - - + -
157I VAL* 4.5 4.9 - - + -
176I TYR* 4.3 0.7 - - - -
238I VAL* 3.5 28.7 - - + +
239I VAL* 1.3 72.6 - - - +
241I THR* 1.4 58.9 + - - +
269I ILE* 3.7 28.3 - - + +
271I VAL* 3.9 22.9 - - + -
302I PHE* 4.8 0.2 - - + -
305I LEU* 4.4 9.0 - - + -
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Residues in contact with THR 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I ASP* 3.2 16.7 + - - -
153I MET* 6.0 0.2 - - - -
176I TYR* 2.7 27.3 + - - +
209I THR* 4.3 0.9 - - - +
211I THR* 5.4 1.3 - - + -
239I VAL* 4.9 4.7 - - + -
240I ILE* 1.4 72.5 - - - +
242I ASP* 1.3 55.3 + - - +
243I GLY 3.2 15.7 + - - +
268I VAL* 4.7 15.3 - - + -
269I ILE 3.2 14.2 + - - +
271I VAL* 3.0 28.0 + - - +
275I PHE* 3.6 24.0 - - + -
284I LEU* 4.9 1.8 - - + -
287I ILE* 4.9 9.6 - - + -
302I PHE* 5.2 1.3 - - - -
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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