Contacts of the strand formed by residues 270 - 275 (chain D) in PDB entry 1SXG
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 GLU 270 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172D LEU* 3.9 10.5 - - + +
175D SER* 4.5 6.9 - - - +
177D HIS* 2.9 33.2 + - + +
241D THR 3.6 4.9 + - - -
242D ALA* 3.2 11.7 - - + -
243D ILE 2.8 26.0 + - - -
266D PRO* 3.5 12.1 - - + +
269D LEU* 1.3 74.7 - - - +
271D ILE* 1.3 64.0 + - - +
272D ILE* 4.7 0.9 - - - -
330D SER 3.4 6.5 - - - +
331D THR* 3.1 16.9 - - - +
332D LYS* 2.6 51.6 + - - +
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Residues in contact with ILE 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D ILE* 3.3 13.5 - - + +
245D VAL* 4.0 20.9 - - + -
251D ALA 4.6 2.2 - - - +
254D VAL* 3.7 22.4 - - + +
255D ILE* 3.4 42.6 - - + -
258D ALA* 5.1 0.4 - - + -
265D VAL* 3.7 19.3 - - + -
269D LEU* 3.9 12.3 - - + +
270D GLU* 1.3 81.9 - - - +
272D ILE* 1.3 68.9 + - - +
287D LEU* 4.6 7.4 - - + -
288D THR* 3.8 2.8 - - - +
330D SER* 2.3 44.1 + - - +
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Residues in contact with ILE 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ALA* 3.9 15.9 - - + +
171D SER* 4.4 11.2 - - - +
172D LEU* 3.3 38.4 - - + -
243D ILE 3.0 8.1 + - - +
244D PHE* 3.4 21.6 - - + -
245D VAL 2.7 31.5 + - - -
271D ILE* 1.3 81.0 - - - +
273D GLY* 1.3 69.9 + - - +
287D LEU* 4.5 0.9 - - - -
288D THR* 3.3 19.3 - - + +
289D SER* 4.7 1.3 - - - -
290D VAL* 4.3 3.6 - - + -
325D ILE* 5.4 3.1 - - + -
327D PHE* 5.6 0.9 - - + -
331D THR* 3.0 28.3 - - + +
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Residues in contact with GLY 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D PHE* 4.2 0.3 - - - -
245D VAL 3.6 7.2 - - - -
248D ASP* 4.0 6.1 - - - -
251D ALA* 4.1 8.7 - - - -
272D ILE* 1.3 83.5 - - - +
274D PHE* 1.3 61.5 + - - +
287D LEU* 3.8 13.5 - - - +
288D THR 2.7 15.7 + - - -
289D SER* 3.2 9.4 - - - -
290D VAL* 2.9 19.9 + - - +
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Residues in contact with PHE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ILE* 4.2 3.8 - - + -
161D TYR* 3.8 20.4 - + - -
164D ALA* 3.8 28.7 - - + -
165D ALA* 4.1 9.0 - - - -
196D LYS* 3.6 25.8 - - + -
244D PHE* 3.9 15.0 - + + -
245D VAL 3.6 9.6 + - - +
246D GLY 3.1 20.2 - - - +
247D THR* 3.4 3.3 - - - -
248D ASP* 3.3 12.7 + - - -
273D GLY* 1.3 75.0 - - - +
275D ASP* 1.3 88.4 + - - +
289D SER* 3.1 6.0 + - - -
290D VAL* 3.7 20.9 - - + -
292D GLN* 3.2 31.0 - - + -
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Residues in contact with ASP 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D PHE* 3.3 28.2 - - + +
77D GLU* 5.4 1.0 - - - +
196D LYS* 5.0 1.4 + - - -
246D GLY 4.7 0.6 - - - +
247D THR* 3.7 21.8 - - - +
248D ASP* 3.7 6.2 + - - +
274D PHE* 1.3 92.2 - - - +
276D ASN* 1.3 70.3 + - - +
277D THR* 3.8 19.9 - - + +
290D VAL 2.6 15.5 + - - -
291D VAL* 4.9 0.3 - - - +
292D GLN* 3.0 52.8 + - - +
293D PRO* 5.4 0.3 - - - +
294D MET* 5.2 1.6 - - + +
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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