Contacts of the strand formed by residues 293 - 300 (chain D) in PDB entry 1RG9
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 ARG 293 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D TYR* 3.7 15.5 + - - +
126D ALA 3.3 14.8 - - - +
127D THR* 4.1 13.0 - - - +
286D VAL* 3.9 2.7 - - - -
291D ALA* 3.3 1.0 - - - -
292D ASP* 1.3 83.8 - - + +
294D CYS* 1.3 64.2 + - - +
314D THR* 3.3 10.9 - - - +
315D PHE* 3.2 67.3 + - + +
317D THR* 3.1 17.6 + - + +
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Residues in contact with CYS 294 (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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125D TYR* 3.5 7.1 - - - -
126D ALA 3.2 27.9 + - - -
282D ALA* 3.8 19.5 - - - +
285D ILE* 3.7 39.5 - - - -
286D VAL* 4.3 3.5 - - + +
291D ALA* 4.4 3.4 - - + -
293D ARG* 1.3 77.0 - - - +
295D GLU* 1.3 59.4 + - - +
296D ILE* 4.5 7.4 - - - -
312D VAL* 5.5 2.5 - - - -
313D GLU 3.0 13.0 - - - +
314D THR* 3.5 18.8 - - + -
315D PHE* 3.8 1.5 - - - -
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Residues in contact with GLU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ARG* 5.6 0.7 - - - -
123D PHE* 3.9 15.4 - - + -
124D GLY 3.3 11.0 - - - +
125D TYR* 3.5 15.6 - - + -
254D MET 4.8 0.7 - - - +
255D ALA* 3.3 11.6 - - + -
256D ARG* 2.7 65.7 + - - +
294D CYS* 1.3 73.2 - - - +
296D ILE* 1.3 61.8 + - - +
311D MET* 3.7 4.2 - - + +
312D VAL* 3.6 2.1 - - - +
313D GLU* 2.7 46.4 + - + +
315D PHE* 3.8 20.2 - - + -
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Residues in contact with ILE 296 (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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123D PHE* 3.3 10.8 - - - -
124D GLY 2.8 29.9 + - - +
278D ALA* 4.1 30.3 - - + +
281D VAL* 3.6 31.2 - - + -
282D ALA* 4.5 7.4 - - + -
285D ILE* 4.6 1.1 - - + -
294D CYS* 4.1 7.4 + - - -
295D GLU* 1.3 75.8 - - - +
297D GLN* 1.3 72.1 + - - +
298D VAL* 4.7 9.2 - - + +
310D ILE* 5.1 4.0 - - + -
311D MET* 3.4 4.0 - - - +
312D VAL* 3.4 37.5 - - + -
329D VAL* 4.5 11.2 - - + -
335D LEU* 6.2 1.6 - - + -
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Residues in contact with GLN 297 (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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4C LEU 4.1 5.4 + - - -
5C PHE* 3.6 12.3 - - - -
6C THR* 3.1 39.7 + - - +
121D LEU* 3.5 8.7 - - + +
122D MET 3.2 11.9 - - - +
123D PHE* 3.2 38.0 - - + -
296D ILE* 1.3 79.5 - - - +
298D VAL* 1.3 69.1 + - - +
309D SER* 4.1 3.2 + - - -
310D ILE* 3.1 6.9 - - - +
311D MET* 3.0 56.5 + - + +
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Residues in contact with VAL 298 (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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121D LEU* 3.2 3.3 - - - +
122D MET* 2.7 58.5 + - + +
274D ALA* 4.1 13.7 - - + +
278D ALA* 4.8 6.1 - - + -
296D ILE* 4.8 7.0 - - + -
297D GLN* 1.3 77.7 - - - +
299D SER* 1.3 58.5 + - - +
300D TYR* 3.9 16.8 - - + +
307D PRO* 5.1 2.2 - - + -
309D SER* 3.1 6.3 - - - +
310D ILE* 3.7 27.8 - - + -
335D LEU* 4.0 26.7 - - + -
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Residues in contact with SER 299 (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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6C THR* 3.3 33.7 + - - +
167C GLN* 3.6 2.0 - - - -
120D GLY 2.9 12.8 - - - -
121D LEU* 4.0 3.6 - - - -
298D VAL* 1.3 76.1 - - - +
300D TYR* 1.3 69.6 + - - +
307D PRO* 3.7 2.8 - - - +
308D THR* 2.4 47.5 + - - -
309D SER* 3.1 23.4 + - - -
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Residues in contact with TYR 300 (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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167C GLN* 2.7 20.1 + - - -
116D ALA* 3.9 20.2 - - + -
118D ASP 4.0 6.3 - - - +
119D GLN* 3.1 3.8 - - - -
120D GLY 2.6 24.6 + - - +
122D MET* 4.0 11.0 - - - -
270D VAL* 3.8 22.4 - - + -
274D ALA* 3.3 34.5 - - + +
298D VAL* 3.9 18.1 - - + +
299D SER* 1.3 77.5 - - - +
301D ALA* 1.3 61.6 + - - +
304D VAL 4.8 1.8 - - - -
305D ALA 4.6 1.1 - - - -
306D GLU 4.9 0.2 - - - -
307D PRO* 3.8 26.9 - - + -
308D THR* 3.6 6.5 - - - +
335D LEU* 2.6 37.5 + - - +
337D PRO* 4.2 11.7 - - + -
340D LEU* 3.4 7.4 - - - +
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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