Contacts of the strand formed by residues 277 - 287 (chain A) in PDB entry 1R00
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 LEU 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A THR* 5.7 0.4 - - - -
249A ALA 3.7 9.6 - - - +
250A ASP 4.3 0.4 - - - +
252A VAL* 3.8 17.9 - - + +
273A CYS 3.0 9.5 + - - +
274A VAL* 3.0 21.2 + - - +
275A ARG 4.4 3.3 - - - +
276A ALA* 1.3 76.5 - - - +
278A GLU* 1.3 72.9 + - - +
279A PRO* 3.8 2.4 - - - +
281A GLY* 3.8 18.2 - - - +
282A ARG 3.3 34.3 - - - +
283A LEU* 4.0 15.7 - - + +
331A LEU* 4.7 7.2 - - + -
354A THR 5.0 0.2 - - - -
355A ALA* 4.4 26.0 - - + +
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Residues in contact with GLU 278 (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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184A ARG* 4.5 8.5 + - - -
185A HIS* 4.8 3.7 - - - +
248A THR* 2.7 38.9 + - + +
249A ALA* 3.1 29.9 + - - +
250A ASP* 3.9 17.5 + - + +
276A ALA 3.3 0.4 + - - -
277A LEU* 1.3 77.1 - - - +
279A PRO* 1.3 80.0 - - + +
280A GLY 3.3 0.2 + - - -
281A GLY* 2.9 17.0 + - - -
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Residues in contact with PRO 279 (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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250A ASP* 6.0 0.7 - - - +
277A LEU 3.8 3.1 - - - +
278A GLU* 1.3 91.6 - - + +
280A GLY* 1.3 61.5 + - - +
281A GLY* 3.3 0.7 + - - -
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Residues in contact with GLY 280 (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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278A GLU 3.3 0.2 + - - -
279A PRO* 1.3 71.6 - - - +
281A GLY* 1.3 60.1 + - - +
282A ARG* 3.0 24.9 + - - +
354A THR* 5.6 1.6 - - - -
355A ALA* 6.2 1.8 - - - +
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Residues in contact with GLY 281 (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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250A ASP* 3.2 23.1 - - - -
277A LEU* 3.8 16.6 - - - +
278A GLU 2.9 17.3 + - - -
279A PRO 3.2 1.4 + - - -
280A GLY* 1.3 82.2 - - - +
282A ARG* 1.3 70.6 + - - -
353A PHE 4.0 0.9 - - - +
354A THR* 4.0 8.5 - - - +
355A ALA 4.7 0.7 + - - -
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Residues in contact with ARG 282 (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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178A TYR* 4.0 10.5 - - - +
250A ASP 2.9 10.0 + - - +
251A VAL* 3.1 13.7 - - + +
252A VAL 3.0 23.2 + - - +
277A LEU* 3.3 5.6 - - - +
280A GLY* 3.0 28.4 + - - +
281A GLY* 1.3 75.4 - - - -
283A LEU* 1.3 58.8 + - - +
284A LEU* 4.0 4.0 - - + -
334A ALA* 4.8 5.2 - - - +
352A GLU* 3.4 38.8 + - + +
353A PHE 3.5 5.4 - - - +
354A THR* 3.3 35.6 - - - +
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Residues in contact with LEU 283 (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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252A VAL* 3.3 14.8 - - + +
254A LEU* 4.4 4.9 - - + -
270A LEU* 4.0 16.2 - - + +
273A CYS* 3.5 33.0 - - + -
274A VAL* 4.4 7.6 - - - +
277A LEU* 4.0 8.5 - - + +
282A ARG* 1.3 71.1 - - - +
284A LEU* 1.3 67.3 + - - +
285A VAL* 3.8 25.1 - - + -
331A LEU* 3.9 31.0 - - + -
351A LEU 3.6 1.2 - - - +
352A GLU* 3.5 2.6 - - - -
353A PHE* 2.9 47.3 + - + +
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Residues in contact with LEU 284 (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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178A TYR* 3.7 29.2 - - + +
180A TRP* 3.5 36.3 - - + -
251A VAL* 4.1 17.5 - - + -
252A VAL 2.8 8.8 + - - +
253A LEU* 3.5 13.8 - - + +
254A LEU* 2.9 26.7 + - - +
282A ARG* 4.2 5.4 - - + -
283A LEU* 1.3 78.8 - - - +
285A VAL* 1.3 62.5 + - - +
286A LEU* 3.9 0.4 - - + -
350A ILE* 4.3 12.1 - - + -
351A LEU 3.3 5.2 - - - +
352A GLU* 3.5 34.8 - - + -
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Residues in contact with VAL 285 (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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254A LEU* 3.4 13.0 - - + +
258A LEU* 3.8 33.7 - - + -
270A LEU* 5.0 2.0 - - + -
283A LEU* 3.8 18.2 - - + -
284A LEU* 1.3 73.7 - - - +
286A LEU* 1.3 60.8 + - - +
287A ASP* 4.1 23.1 - - + +
322A VAL* 4.6 6.5 - - + -
349A SER 3.3 4.5 - - - +
350A ILE* 3.3 1.8 - - - -
351A LEU* 2.8 52.7 + - + +
353A PHE* 3.9 16.2 - - + -
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Residues in contact with LEU 286 (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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171A TYR* 4.6 2.2 - - + -
174A PRO* 3.7 26.0 - - + -
196A MET* 3.9 31.4 - - + -
253A LEU* 4.5 7.6 - - + +
254A LEU 3.0 8.1 + - - +
255A SER* 3.4 28.5 - - - +
256A PHE* 2.8 44.8 + - + -
284A LEU* 3.9 2.2 - - + +
285A VAL* 1.3 70.2 - - - +
287A ASP* 1.3 67.0 + - - +
348A PHE* 3.9 25.1 - - + -
349A SER 3.4 4.9 - - - +
350A ILE* 4.0 14.8 - - + +
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Residues in contact with ASP 287 (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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256A PHE* 3.4 34.2 - - - -
257A VAL 3.8 2.9 + - - -
258A LEU* 3.8 9.1 + - - +
259A LEU* 3.6 48.4 + - - +
285A VAL* 3.9 13.1 - - + +
286A LEU* 1.3 75.1 - - - +
288A ARG* 1.3 77.4 + - - +
322A VAL* 6.4 2.5 - - + -
348A PHE* 3.6 5.0 - - - +
349A SER* 3.0 23.3 + - - +
351A LEU* 6.2 1.3 - - + -
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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