Contacts of the strand formed by residues 239 - 246 (chain A) in PDB entry 1SEK
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 ALA 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A LYS 4.7 4.7 + - - +
98A VAL* 4.0 30.7 - - + -
233A SER* 3.8 2.8 - - - -
234A TYR* 3.1 30.7 + - + +
237A ASP 4.7 0.7 - - - -
238A GLN* 1.3 82.1 + - - +
240A SER* 1.3 64.7 + - - +
371A LEU* 4.9 8.3 - - + -
372A LYS 3.2 10.8 - - - +
373A TYR* 4.3 15.9 - - + +
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Residues in contact with SER 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLU* 3.8 30.0 + - - +
232A MET 3.1 15.6 + - - -
233A SER* 3.2 19.6 - - - +
234A TYR* 4.2 7.0 - - - -
239A ALA* 1.3 72.7 + - - +
241A MET* 1.3 60.1 + - - +
242A ILE 4.0 0.2 - - - -
370A SER 3.8 0.5 - - - +
371A LEU* 3.6 3.8 - - - +
372A LYS* 2.9 41.0 + - - +
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Residues in contact with MET 241 (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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180A PHE* 4.6 5.2 - - + -
184A TRP* 3.9 24.5 - - + -
230A ILE 3.7 0.7 - - - +
231A GLU* 3.4 3.8 - - - -
232A MET* 2.7 35.4 + - + +
234A TYR* 3.5 23.4 - - + +
240A SER* 1.3 70.9 - - - +
242A ILE* 1.3 68.0 + - - +
243A ILE* 3.9 21.7 + - + -
281A LEU* 6.2 0.2 - - + -
284A PHE* 5.1 3.1 - - + -
333A ILE* 6.0 0.2 - - + -
335A VAL* 4.0 23.3 - - + -
369A PHE* 4.1 24.5 - - + -
370A SER 3.7 17.3 - - - +
371A LEU* 4.6 10.8 - - + -
379A PHE* 4.8 5.6 - - + -
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Residues in contact with ILE 242 (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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229A MET* 3.7 33.2 - - + -
230A ILE 3.5 4.3 - - - +
231A GLU* 2.9 39.9 - - + +
240A SER 4.9 0.2 - - - +
241A MET* 1.3 75.0 - - - +
243A ILE* 1.3 64.6 + - - +
244A ILE* 4.2 11.4 - - + -
265A LEU* 5.2 4.7 - - + -
269A GLU* 4.1 13.9 - - - +
272A LEU* 4.7 0.4 - - + -
368A PHE* 4.8 7.4 - - + -
369A PHE* 3.1 7.1 - - - +
370A SER* 2.8 43.9 + - - +
372A LYS* 4.6 23.3 - - + -
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Residues in contact with ILE 243 (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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228A LYS 3.7 1.0 - - - +
229A MET* 3.3 2.9 - - - +
230A ILE* 2.7 50.2 + - + +
232A MET* 3.3 33.7 - - + -
241A MET* 4.1 14.6 - - + +
242A ILE* 1.3 78.6 - - - +
244A ILE* 1.3 72.4 + - - +
245A LEU 4.4 1.6 - - - +
281A LEU* 4.2 20.6 - - + -
284A PHE* 6.3 0.9 - - + -
363A ILE* 4.0 28.0 - - + -
367A PHE* 4.2 16.6 - - + -
368A PHE 3.5 9.2 - - - +
369A PHE* 4.6 6.5 - - + -
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Residues in contact with ILE 244 (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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222A VAL* 6.1 0.4 - - + -
225A LEU* 4.1 17.3 - - + -
227A ALA* 3.6 20.4 - - + -
228A LYS 3.4 6.1 - - - +
229A MET* 3.6 23.1 - - + -
242A ILE* 4.2 2.7 - - + -
243A ILE* 1.3 78.6 - - - +
245A LEU* 1.3 60.9 + - - +
246A PRO* 3.6 5.5 - - - +
255A LEU* 3.6 23.7 - - + +
259A LEU* 4.9 4.9 - - + -
265A LEU* 3.6 31.4 - - + -
367A PHE* 3.6 1.6 - - - +
368A PHE* 2.9 51.3 + - + +
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Residues in contact with LEU 245 (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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227A ALA* 3.6 2.2 - - - -
228A LYS* 2.8 57.1 + - + +
230A ILE* 4.9 1.3 - - + -
243A ILE* 4.0 1.1 - - + -
244A ILE* 1.3 73.6 - - - +
246A PRO* 1.3 74.8 - - + +
247A ASN 3.6 0.2 + - - -
361A VAL* 5.3 3.8 - - + -
362A GLU 3.4 24.2 - - - +
363A ILE* 4.0 35.7 - - + -
365A LYS* 3.5 54.1 - - + +
367A PHE* 4.0 4.5 - - + -
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Residues in contact with PRO 246 (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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225A LEU 5.5 0.7 - - - +
226A ASP 3.7 3.4 - - - +
227A ALA* 3.6 11.9 - - + -
244A ILE 3.6 9.2 - - - +
245A LEU* 1.3 89.4 - - + +
247A ASN* 1.3 64.7 + - - +
248A GLN 3.4 17.5 + - - +
249A VAL 5.6 0.4 - - - +
251A GLY* 3.8 20.0 - - - +
252A ILE* 3.8 17.0 - - + +
255A LEU* 4.7 11.2 - - + -
365A LYS* 3.2 18.8 + - + +
366A PRO 3.3 27.6 - - - +
367A PHE* 4.3 0.9 - - - -
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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