Contacts of the strand formed by residues 246 - 251 (chain A) in PDB entry 3SOQ
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 SER 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A THR* 3.6 3.6 - - - -
241A ASP 3.1 26.6 + - - -
244A THR* 2.7 24.3 + - - -
245A HIS* 1.3 78.8 - - - +
247A ILE* 1.3 65.2 + - - +
248A LEU* 3.6 8.1 - - - +
260A GLU* 2.7 35.2 + - - -
262A HIS 3.2 13.9 - - - -
263A SER* 3.9 3.6 - - - -
265A ILE* 3.9 5.6 - - - -
268A PRO* 4.0 2.5 - - - +
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Residues in contact with ILE 247 (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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23A LEU* 4.2 14.8 - - + -
25A TYR* 3.7 35.2 - - + -
34A VAL* 4.3 7.9 - - + -
238A TYR* 4.6 1.6 - - + -
239A TRP 3.3 10.8 - - - +
240A THR* 4.0 14.4 - - + -
246A SER* 1.3 77.6 - - - +
248A LEU* 1.3 67.4 + - - +
260A GLU* 3.7 3.8 - - - +
261A ILE* 2.8 37.9 + - + -
262A HIS* 2.8 26.4 + - + +
265A ILE* 3.8 13.7 - - + -
271A ILE* 3.8 23.1 - - + -
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Residues in contact with LEU 248 (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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224A LEU* 5.9 1.1 - - + -
225A PRO* 6.4 0.9 - - + -
238A TYR* 3.3 5.2 - - - +
239A TRP* 2.8 63.9 + - + +
241A ASP* 3.7 17.7 - - + -
244A THR* 3.6 15.3 - - + +
246A SER* 3.6 18.4 - - - +
247A ILE* 1.3 78.5 - - - +
249A ALA* 1.3 62.5 + - - +
258A LEU* 4.5 9.9 - - + -
259A ARG 3.4 5.6 - - - +
260A GLU* 3.6 39.9 - - + +
261A ILE* 4.2 2.0 - - - -
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Residues in contact with ALA 249 (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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236A ILE* 3.9 6.5 - - + -
237A LEU 3.1 12.8 - - - +
238A TYR* 3.7 13.0 - - + -
239A TRP* 3.9 4.3 - - - -
248A LEU* 1.3 76.0 - - - +
250A CYS* 1.3 65.8 + - - +
257A GLY 3.5 2.1 - - - +
258A LEU* 3.2 3.1 - - - +
259A ARG* 2.8 41.9 + - - +
261A ILE* 3.6 27.6 - - + -
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Residues in contact with CYS 250 (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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220A VAL* 3.6 22.4 - - - -
236A ILE* 3.4 9.4 - - - -
237A LEU* 2.9 43.0 + - - -
239A TRP* 3.5 24.9 - - + -
249A ALA* 1.3 78.2 - - - +
251A ASN* 1.3 71.0 + - - +
255A GLY* 3.7 11.0 - - - +
256A GLU 3.6 13.9 - - - +
257A GLY 4.0 4.7 - - - -
258A LEU* 4.0 6.7 - - + -
259A ARG* 4.2 1.8 - - - +
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Residues in contact with ASN 251 (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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219A VAL* 4.0 1.0 - - - +
235A ASP* 3.6 23.6 + - - +
236A ILE* 4.2 9.0 - - + +
250A CYS* 1.3 73.2 - - - +
252A LYS* 1.3 60.6 + - - +
253A TYR* 2.8 35.2 + - - +
254A THR* 3.1 24.4 + - - +
255A GLY* 2.8 29.5 + - - -
256A GLU* 2.9 21.0 + - + +
259A ARG* 4.7 1.2 - - - +
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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