Contacts of the strand formed by residues 270 - 275 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172I LEU* 4.4 9.8 - - + +
175I SER* 4.1 8.2 + - - -
177I HIS* 2.8 37.0 + - + +
241I THR 2.9 7.1 + - - -
242I ALA* 2.9 10.8 - - + +
243I ILE 2.8 24.3 + - - +
266I PRO* 3.1 25.7 - - + +
269I LEU* 1.3 73.5 - - - +
271I ILE* 1.3 61.6 + - - +
330I SER 3.7 6.7 - - - +
331I THR* 3.3 10.2 + - - +
332I LYS* 2.9 49.8 + - - +
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Residues in contact with ILE 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243I ILE* 3.2 18.2 - - + +
245I VAL* 4.4 10.1 - - + -
251I ALA* 4.5 2.2 - - + +
254I VAL* 3.4 30.5 - - + +
255I ILE* 4.0 16.6 - - + -
265I VAL* 4.2 16.6 - - + -
269I LEU* 3.2 34.5 + - + -
270I GLU* 1.3 72.7 - - - +
272I ILE* 1.3 71.6 + - - +
287I LEU* 3.5 25.6 - - + -
288I THR* 4.3 0.3 - - - -
330I SER* 2.5 38.3 + - - +
331I THR* 4.5 0.5 + - - -
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Residues in contact with ILE 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I ALA* 3.5 42.0 - - + +
171I SER* 3.7 17.5 - - - +
172I LEU* 3.8 21.8 - - + -
243I ILE 3.0 9.3 + - - +
244I PHE* 3.6 9.8 - - + -
245I VAL* 2.9 26.0 + - - +
271I ILE* 1.3 81.9 - - - +
273I GLY* 1.3 71.9 + - - +
288I THR* 3.2 30.7 - - + +
289I SER* 4.5 0.7 - - - -
290I VAL* 4.4 5.6 - - + -
325I ILE* 5.1 2.2 - - + -
327I PHE* 4.9 1.6 - - + -
331I THR* 4.5 7.4 - - - +
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Residues in contact with GLY 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I PHE* 4.2 1.6 - - - -
245I VAL 3.5 9.5 - - - +
251I ALA* 4.0 9.2 - - - -
272I ILE* 1.3 81.4 - - - +
274I PHE* 1.3 63.5 + - - +
287I LEU* 3.7 21.7 - - - +
288I THR 2.6 15.3 + - - -
289I SER* 3.4 6.5 - - - -
290I VAL* 3.1 17.5 + - - +
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Residues in contact with PHE 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159I ILE* 4.0 4.7 - - + -
161I TYR* 3.7 31.6 - + - -
164I ALA* 3.7 29.4 - - + -
165I ALA* 4.2 8.3 - - - -
196I LYS* 4.1 21.5 - - + -
244I PHE* 3.9 16.6 - + - -
245I VAL 3.7 3.6 + - - +
246I GLY* 3.4 21.8 - - - +
247I THR* 3.7 0.5 - - - -
248I ASP* 2.9 22.2 + - - +
273I GLY* 1.3 72.2 - - - -
275I ASP* 1.3 97.7 + - - +
289I SER* 3.1 9.8 + - - -
290I VAL* 3.6 24.5 - - + +
292I GLN* 3.6 20.0 - - + -
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Residues in contact with ASP 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I PHE* 3.3 35.1 - - + +
196I LYS* 5.2 1.7 + - - -
246I GLY 5.0 0.8 - - - +
247I THR* 4.1 13.7 + - - +
248I ASP 4.6 1.9 + - - -
274I PHE* 1.3 90.9 - - - +
276I ASN* 1.3 69.4 + - - +
277I THR* 3.4 20.7 - - + +
290I VAL 2.7 13.4 + - - -
292I GLN* 2.7 54.5 + - - +
294I MET* 3.8 4.7 - - - +
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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
------------------------------------------------------------
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