Contacts of the strand formed by residues 233 - 245 (chain A) in PDB entry 3RT0
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 HIS 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A LYS* 2.9 53.6 - - + +
215A LEU 3.0 24.2 - - - +
216A PRO* 4.2 2.0 - - + -
217A ILE* 3.4 9.5 - - - +
232A THR* 1.3 103.3 + - - +
234A LEU* 1.3 63.0 + - - +
235A THR* 4.3 2.3 + - - -
270A LYS* 6.2 4.3 - - + -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 3.2 56.1 - - + +
184A LEU 6.0 1.1 - - - +
214A LYS* 3.7 1.7 - - - -
215A LEU* 2.9 31.8 + - + +
217A ILE* 3.2 23.2 - - + +
220A LEU* 3.8 16.8 - - + -
233A HIS* 1.3 81.0 - - - +
235A THR* 1.3 67.2 - - - +
335A CYS* 4.1 12.1 - - + -
336A SER* 4.4 9.4 - - - +
337A SER* 3.7 20.4 - - - +
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Residues in contact with THR 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A CYS* 4.9 9.0 - - - +
211A HIS* 3.5 46.6 + - + +
213A LEU 3.5 8.3 - - - +
214A LYS* 5.0 4.3 - - - +
233A HIS* 4.3 2.8 + - - -
234A LEU* 1.3 72.3 - - - +
236A GLY* 1.3 60.9 + - - +
237A HIS* 4.0 11.7 + - + -
334A VAL 4.0 0.3 - - - +
335A CYS* 3.3 23.4 - - - +
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Residues in contact with GLY 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A HIS 3.9 0.5 - - - -
212A PHE* 3.1 10.0 + - - +
213A LEU* 2.8 41.5 + - - +
215A LEU* 3.8 20.9 - - - -
234A LEU 3.5 1.6 + - - -
235A THR* 1.3 75.3 - - - +
237A HIS* 1.3 63.9 + - - -
333A LEU* 5.9 0.7 - - - -
334A VAL 3.5 6.5 - - - -
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Residues in contact with HIS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A CYS* 3.0 40.5 + - - +
188A PRO* 3.5 30.4 - - + +
209A SER 3.8 3.6 - - - -
210A PRO* 3.7 5.4 - - + -
211A HIS* 2.8 49.7 + - - -
213A LEU* 5.6 0.4 - - - -
235A THR* 4.0 9.2 + - + +
236A GLY* 1.3 74.0 - - - -
238A PHE* 1.3 61.4 + - - +
239A PHE* 3.7 22.9 - + + -
332A ALA 3.5 1.7 - - - +
333A LEU* 3.2 8.9 - - - +
334A VAL* 2.9 43.7 + - + +
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Residues in contact with PHE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ALA* 3.9 12.3 - - + -
208A VAL* 3.4 2.9 - - - +
209A SER* 2.9 47.5 + - - +
212A PHE* 4.4 10.5 - - + -
213A LEU* 4.8 3.6 - - + -
236A GLY 4.2 0.2 + - - -
237A HIS* 1.3 72.5 - - - +
239A PHE* 1.3 69.4 + - - +
240A GLY 3.8 12.3 - - - -
242A TYR* 3.3 26.5 - - - -
258A LEU* 4.3 4.3 - - + -
259A HIS* 3.5 44.2 - + + -
262A LEU* 3.9 18.4 - - + -
331A VAL* 4.0 24.9 - - + -
332A ALA 3.7 2.0 - - - -
333A LEU* 3.9 19.3 - - + -
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Residues in contact with PHE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PRO* 4.8 7.4 - - + -
189A LEU 5.5 0.2 - - - -
190A TRP* 3.8 29.4 - + + -
207A ALA 3.6 4.0 - - - -
208A VAL* 3.6 32.5 - - + -
210A PRO* 6.1 0.4 - - + -
237A HIS* 3.7 30.1 - + + -
238A PHE* 1.3 82.8 - - - +
240A GLY* 1.3 57.9 + - - +
331A VAL* 3.3 3.8 - - - +
332A ALA* 2.8 47.2 + - + +
334A VAL* 3.9 18.2 - - + -
429A LEU* 3.6 15.8 - - + +
497A ILE* 4.0 10.1 - - + -
499A ILE* 3.6 38.6 - - + -
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Residues in contact with GLY 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PHE* 3.3 5.9 - - - +
207A ALA 2.9 35.1 + - - +
238A PHE* 3.8 2.8 - - - -
239A PHE* 1.3 76.5 - - - +
241A VAL* 1.3 64.8 + - - +
242A TYR* 3.8 22.4 - - - -
330A VAL 3.4 8.1 - - - -
331A VAL* 4.2 1.8 - - - -
429A LEU* 4.4 0.2 - - - -
497A ILE* 3.7 3.2 - - - +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ASP* 5.6 0.2 - - - +
205A ALA 3.9 4.0 - - - +
206A PHE* 4.6 4.3 - - + -
240A GLY* 1.3 76.4 - - - +
242A TYR* 1.3 69.2 + - - +
243A ASP 4.1 1.4 + - - +
328A THR* 4.5 1.6 + - - -
329A ALA* 3.6 1.0 - - - -
330A VAL* 2.9 44.0 + - + +
347A SER* 4.9 1.5 + - - +
429A LEU* 3.8 23.1 - - + +
430A ALA* 4.1 1.8 - - - -
431A SER* 3.8 30.7 - - - +
495A SER* 4.2 20.0 - - - +
497A ILE* 3.5 27.8 - - + +
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Residues in contact with TYR 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ASP* 3.6 2.3 - - - +
205A ALA 2.8 45.3 + - - +
206A PHE* 4.1 0.2 - - - -
207A ALA* 4.3 8.0 - - + +
238A PHE* 3.3 32.2 - - - -
240A GLY* 3.8 17.4 - - - -
241A VAL* 1.3 83.2 - - - +
243A ASP* 1.3 61.4 + - - +
244A GLY 3.3 4.9 + - - -
251A ALA* 3.6 16.9 - - + +
254A CYS* 3.6 24.0 + - + -
255A ARG* 3.7 30.5 - - - -
258A LEU* 3.9 14.8 - - + +
259A HIS* 5.0 0.5 + - - -
327A SER* 3.4 12.1 - - - +
328A THR 3.5 3.1 - - - -
329A ALA* 3.7 26.0 - - + -
331A VAL* 3.9 9.0 - - + +
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ASP* 3.2 16.0 - - - +
241A VAL 4.1 0.4 - - - -
242A TYR* 1.3 71.2 - - - +
244A GLY* 1.3 69.7 + - - +
245A HIS* 3.8 5.9 + - - -
327A SER* 3.3 3.6 + - - -
328A THR* 3.0 41.6 + - - +
346A ASP* 4.9 2.6 - - - +
347A SER* 3.3 11.0 + - - +
431A SER* 3.8 11.4 - - - -
432A ASP* 3.1 26.2 + - - +
512A MG 2.6 30.2 - - - -
81C SER* 5.0 0.2 + - - -
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Residues in contact with GLY 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLU* 2.8 31.5 + - - +
242A TYR 3.3 2.6 + - - -
243A ASP* 1.3 84.6 + - - +
245A HIS* 1.3 59.3 + - - +
247A GLY 3.9 8.1 - - - -
251A ALA* 3.9 6.3 - - - +
326A GLY 3.5 10.8 - - - -
327A SER* 3.5 7.8 + - - -
81C SER* 3.1 14.4 + - - -
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Residues in contact with HIS 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A GLU* 3.5 4.0 - - - -
243A ASP 3.8 8.7 + - - -
244A GLY* 1.3 73.9 - - - +
246A GLY* 1.3 60.1 + - - +
247A GLY 3.1 6.5 + - - +
324A THR 5.1 1.3 - - - -
325A VAL* 3.6 0.2 - - - -
326A GLY* 2.9 34.2 + - - +
327A SER* 3.5 20.9 - - - -
328A THR 4.1 1.1 - - - -
394A LEU* 4.2 16.6 - - + +
396A MET* 3.8 33.7 - - + +
399A SER* 3.8 9.4 - - - -
402A ASP* 2.5 40.0 + - - -
404A TYR* 5.8 0.2 - - - -
81C SER* 3.5 12.8 - - - +
82C GLY* 4.0 12.8 - - - -
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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