Contacts of the strand formed by residues 234 - 239 (chain A) in PDB entry 3SRG
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 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ILE* 3.3 8.2 - - - +
229A SER* 2.9 39.2 + - - +
231A ASP* 4.3 8.1 - - - -
232A GLY 3.6 0.6 - - - -
233A LYS* 1.4 105.4 - - + +
235A VAL* 1.3 63.1 + - - +
236A TYR* 4.0 25.6 - - + +
247A VAL* 4.3 2.2 - - + -
248A TYR 3.1 14.4 - - - +
249A GLU* 3.9 17.7 + - + -
250A LYS 4.2 0.2 - - - +
259A LEU* 3.7 30.2 - - + +
311A LEU* 3.6 34.2 - - + +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 5.5 1.3 - - + -
179A TYR* 4.6 10.8 - - + -
226A ILE* 4.0 14.8 - - + -
227A ASN 3.4 9.2 - - - +
228A ILE* 4.2 9.9 - - + -
234A TYR* 1.3 79.2 - - - +
236A TYR* 1.3 64.8 - - - +
237A ILE* 3.9 21.1 - - + -
246A HIS 3.7 0.5 - - - +
247A VAL* 3.5 3.5 - - - -
248A TYR* 2.8 34.0 + - + +
250A LYS* 3.7 28.0 - - + -
256A LEU* 4.0 31.6 - - + -
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Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ILE* 3.2 5.9 - - - +
227A ASN* 2.9 34.8 + - + +
228A ILE 3.9 1.8 - - - -
229A SER* 3.6 36.0 - - - -
234A TYR* 4.0 18.2 - - + +
235A VAL* 1.3 75.1 - - - +
237A ILE* 1.3 65.6 + - - +
245A ILE* 4.4 1.6 - - + -
246A HIS 3.2 4.5 - - - +
247A VAL* 3.9 29.4 - - + -
271A ILE* 3.7 18.6 - - + +
273A VAL* 3.9 22.7 - - + -
278A GLY 4.5 4.6 + - - -
280A LEU* 3.8 32.9 - - + +
310A ILE* 3.8 28.5 - - + +
311A LEU* 5.7 1.2 - - - +
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Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A THR* 4.1 13.9 - - + -
205A VAL* 3.8 29.4 - - + -
217A ALA* 4.7 1.1 - - + -
220A PHE* 4.0 21.8 - - + -
223A ALA* 4.2 3.1 - - + -
225A GLY 3.4 7.6 - - - +
226A ILE* 4.0 7.6 - - + -
235A VAL* 3.9 17.3 - - + -
236A TYR* 1.3 81.7 - - - +
238A ALA* 1.3 71.9 + - - +
245A ILE* 3.3 2.7 - - - +
246A HIS* 2.8 41.0 + - + +
248A TYR* 3.8 30.5 - - + -
256A LEU* 4.4 5.6 - - + -
271A ILE* 3.9 4.0 - - - +
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Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ALA* 3.3 4.2 - - - -
224A ASN* 2.8 26.6 + - + -
225A GLY 2.8 13.2 + - - +
237A ILE* 1.3 76.2 - - - +
239A GLU* 1.3 59.5 + - - +
240A LEU 3.7 0.4 - - - -
244A LYS 3.6 5.4 - - - -
245A ILE* 4.3 2.5 - - + -
268A VAL* 3.8 20.4 - - + +
269A ASP 3.3 26.9 - - - +
271A ILE* 3.6 15.6 - - + +
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ALA* 5.4 0.2 - - - +
219A GLY 4.2 3.5 - - - +
220A PHE* 3.4 19.5 - - + -
221A ASP* 2.6 45.5 + - - +
222A PHE 3.8 2.7 - - - -
223A ALA* 4.3 1.3 - - - +
238A ALA* 1.3 71.6 - - - +
240A LEU* 1.3 65.6 + - - +
242A ALA* 3.2 23.9 + - + +
243A HIS* 3.0 18.7 + - - -
244A LYS* 2.8 24.5 + - + +
246A HIS* 2.6 40.0 + - + +
268A VAL* 3.9 1.0 - - - +
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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