Contacts of the strand formed by residues 303 - 311 (chain R) in PDB entry 2X1X
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 GLY 303 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263R PRO* 3.4 9.9 - - - -
301R ASP 3.4 3.6 + - - -
302R GLN* 1.3 74.1 - - - +
304R LEU* 1.3 60.3 + - - -
305R TYR* 3.4 6.9 - - - -
321R PHE* 3.7 22.3 - - - -
322R VAL 2.9 34.9 + - - -
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Residues in contact with LEU 304 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261R GLU* 3.4 8.3 - - - +
262R TYR* 3.6 1.4 - - - -
263R PRO* 3.1 20.5 - - - +
303R GLY* 1.3 71.2 - - - -
305R TYR* 1.3 61.8 + - - +
306R THR* 3.6 20.9 + - + +
319R SER* 3.8 20.6 - - - +
320R THR* 3.5 21.1 - - - +
321R PHE* 4.4 14.6 - - + +
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Residues in contact with TYR 305 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228R LEU* 4.2 3.6 - - - +
242R LEU* 3.7 15.4 - - + +
244R LEU* 3.6 24.7 - - + -
260R TRP* 4.8 4.3 - + + -
261R GLU 3.3 4.0 - - - -
262R TYR* 3.5 22.8 - + + +
263R PRO* 3.5 13.0 - - + +
264R SER* 4.8 1.7 + - - -
292R LEU* 3.6 30.1 - - + -
294R ILE* 3.7 13.7 - - + +
301R ASP* 2.6 42.2 + - - +
303R GLY 3.4 13.0 - - - -
304R LEU* 1.3 72.1 - - - +
306R THR* 1.3 60.8 + - - +
307R CYS 4.1 1.0 + - - -
318R ASN 3.9 0.7 - - - +
319R SER* 3.1 22.1 - - - -
320R THR* 3.1 16.2 + - + +
322R VAL* 3.7 22.6 - - + +
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Residues in contact with THR 306 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259R ASN 3.8 1.6 - - - +
260R TRP* 3.4 5.7 - - - -
261R GLU* 2.7 53.0 + - - +
304R LEU* 3.6 24.3 + - + +
305R TYR* 1.3 74.3 - - - +
307R CYS* 1.3 59.2 + - - +
308R ALA* 5.2 0.3 - - - +
317R LYS* 4.4 24.5 - - + -
318R ASN 3.4 15.0 - - - +
319R SER* 3.8 9.6 - - - -
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Residues in contact with CYS 307 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226R VAL* 4.2 4.2 - - - +
228R LEU* 3.9 6.5 - - + +
246R CYS* 2.0 48.5 - - - -
258R PHE* 3.9 18.4 - - - -
259R ASN 4.1 0.2 - - - -
260R TRP* 3.7 34.7 - - + -
305R TYR 4.1 1.2 + - - -
306R THR* 1.3 72.1 - - - +
308R ALA* 1.3 61.8 + - - +
309R ALA 4.1 0.7 + - - -
316R LYS 4.1 0.7 - - - +
317R LYS* 3.7 2.2 - - - -
318R ASN 3.0 30.0 + - - +
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Residues in contact with ALA 308 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257R ASP 3.7 0.7 - - - +
258R PHE* 3.2 9.5 - - - -
259R ASN* 2.9 49.8 + - + +
306R THR* 3.8 1.1 + - + +
307R CYS* 1.3 78.2 - - - +
309R ALA* 1.3 59.4 + - - +
310R SER* 4.7 2.4 + - - +
315R THR* 4.6 7.9 - - + -
316R LYS 3.8 3.8 - - - +
317R LYS* 3.7 30.1 - - + -
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Residues in contact with ALA 309 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223R ILE* 3.3 10.8 - - + +
226R VAL* 3.9 18.8 - - + -
248R ALA* 3.8 28.7 - - + -
256R ILE* 3.9 10.1 - - + -
257R ASP 3.9 2.7 - - - -
258R PHE* 4.2 7.6 - - + -
307R CYS 4.1 0.8 + - - -
308R ALA* 1.3 72.4 - - - +
310R SER* 1.3 62.1 + - - +
315R THR* 3.4 3.1 - - - +
316R LYS 3.1 30.5 + - - -
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Residues in contact with SER 310 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E VAL* 5.3 0.3 - - - +
191E PRO* 4.9 15.4 - - - +
255R GLY 3.7 0.5 - - - +
256R ILE* 3.3 7.9 - - - +
257R ASP* 3.0 51.5 + - - +
259R ASN* 5.8 1.9 + - - +
308R ALA* 4.7 3.8 + - - +
309R ALA* 1.3 74.9 + - - +
311R SER* 1.3 59.8 + - - +
312R GLY 4.1 3.0 + - - -
313R LEU 5.7 0.2 - - - -
314R MET 3.7 4.0 - - - -
315R THR* 3.1 26.6 + - - +
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Residues in contact with SER 311 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220R GLY 4.9 0.7 - - - -
221R TYR* 2.4 44.6 + - - +
223R ILE* 3.2 17.7 - - - +
254R VAL* 3.5 31.0 - - - -
255R GLY 3.5 7.4 - - - -
256R ILE* 3.8 7.2 - - - -
310R SER* 1.3 71.9 - - - +
312R GLY* 1.3 60.1 + - - +
313R LEU 3.0 8.7 + - - -
314R MET 3.0 16.3 + - - -
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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