Contacts of the strand formed by residues 270 - 275 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172F LEU* 4.3 17.0 - - + +
175F SER* 4.9 5.2 + - - -
177F HIS* 3.2 38.2 + - + +
241F THR 3.4 2.1 + - - +
242F ALA* 3.5 3.3 - - + -
243F ILE 3.2 18.7 + - - -
266F PRO* 2.6 33.7 - - + +
267F ASN 4.9 0.5 - - - -
268F ASP 5.1 0.3 - - - -
269F LEU* 1.3 74.8 + - - +
271F ILE* 1.3 68.7 + - - +
272F ILE* 5.4 0.2 - - - -
330F SER 2.9 22.0 - - - +
331F THR* 3.6 7.4 + - - +
332F LYS* 3.0 36.3 + - - +
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Residues in contact with ILE 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F ILE* 3.2 18.6 - - + +
245F VAL* 3.8 23.6 - - + -
251F ALA* 4.2 5.4 - - + +
254F VAL* 4.9 7.6 - - + -
255F ILE* 3.4 40.8 - - + -
265F VAL* 4.3 0.9 - - + -
269F LEU* 4.0 19.1 - - + +
270F GLU* 1.3 84.1 - - - +
272F ILE* 1.3 71.7 + - - +
287F LEU* 3.2 25.3 - - + +
288F THR* 3.9 1.4 - - - +
330F SER* 2.8 32.0 + - - +
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Residues in contact with ILE 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F ALA* 4.0 13.9 - - + +
171F SER* 4.5 10.3 - - - +
172F LEU* 3.2 45.8 - - + -
243F ILE 3.1 6.4 + - - +
244F PHE* 3.4 19.9 - - + -
245F VAL* 2.8 29.3 + - - +
271F ILE* 1.3 80.8 - - - +
273F GLY* 1.3 76.6 + - - +
288F THR* 3.1 24.9 - - + +
289F SER* 4.4 1.1 - - - -
290F VAL* 4.3 7.9 - - + +
325F ILE* 5.5 2.9 - - + -
327F PHE* 5.6 1.1 - - + -
331F THR* 3.5 13.7 - - - +
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Residues in contact with GLY 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F PHE* 3.9 1.4 - - - -
245F VAL 3.5 6.1 - - - -
247F THR 4.6 0.2 - - - -
248F ASP* 3.6 9.9 - - - -
251F ALA* 4.0 12.1 - - - -
272F ILE* 1.3 84.4 - - - +
274F PHE* 1.3 63.4 + - - +
287F LEU* 3.3 10.8 - - - +
288F THR 2.5 15.5 + - - -
289F SER* 3.3 5.6 - - - -
290F VAL* 3.1 15.9 + - - +
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Residues in contact with PHE 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F ILE* 4.1 11.4 - - + -
161F TYR* 4.2 15.9 - + - -
164F ALA* 3.6 26.2 - - + -
165F ALA* 4.0 12.6 - - + -
196F LYS* 3.6 25.8 - - - -
244F PHE* 3.5 22.0 - + - -
245F VAL 3.5 12.9 + - - +
246F GLY 3.5 9.6 - - - +
247F THR* 3.7 0.9 - - - -
248F ASP* 3.1 19.8 + - - +
273F GLY* 1.3 73.7 - - - +
275F ASP* 1.3 89.7 + - - +
289F SER* 3.0 8.2 + - - -
290F VAL* 3.5 28.7 - - + +
292F GLN* 3.9 19.7 - - + -
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Residues in contact with ASP 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F PHE* 3.3 26.8 - - + +
196F LYS* 5.0 1.9 + - - -
246F GLY 4.7 2.0 - - - +
247F THR* 4.3 15.6 + - - +
248F ASP* 4.1 4.3 + - - +
274F PHE* 1.3 88.8 - - - +
276F ASN* 1.3 71.2 + - - +
277F THR* 3.8 17.9 - - + +
290F VAL 2.8 12.7 + - - -
291F VAL* 5.2 0.2 - - - +
292F GLN* 2.9 45.0 + - - +
294F MET* 3.6 12.0 - - - +
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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