Contacts of the strand formed by residues 348 - 355 (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 PHE 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A ALA* 3.6 28.5 - - + -
174A PRO* 3.4 46.0 - - + -
177A ALA* 4.2 13.2 - - + -
256A PHE* 4.8 4.3 - - + -
286A LEU* 3.9 13.2 - - + -
287A ASP 3.6 9.9 - - - +
288A ARG* 4.0 1.1 - - - +
337A ARG 4.8 4.0 - - - -
338A THR* 3.2 6.6 - - - -
339A SER* 3.0 59.9 + - - -
340A GLY 3.8 14.6 - - - -
341A SER* 4.6 2.7 - - - -
344A LEU* 4.5 20.6 - - + -
346A PHE* 5.1 0.9 - - + -
347A ASP* 1.3 74.2 - - - +
349A SER* 1.3 68.5 + - - +
350A ILE* 4.6 6.1 - - + -
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Residues in contact with SER 349 (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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285A VAL 3.3 4.2 - - - +
286A LEU* 3.4 1.4 - - - +
287A ASP* 3.0 29.5 + - - +
288A ARG* 4.0 18.8 - - - -
319A ARG* 5.1 5.5 - - - +
336A GLU* 4.1 6.4 + - - +
337A ARG 3.7 6.3 - - - -
338A THR* 3.6 22.4 - - - +
348A PHE* 1.3 82.5 - - - +
350A ILE* 1.3 61.0 + - - +
351A LEU* 4.3 17.2 - - - +
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Residues in contact with ILE 350 (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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174A PRO* 3.5 30.7 - - + +
177A ALA* 4.5 11.4 - - + +
178A TYR* 4.2 34.1 - - + -
180A TRP* 5.4 1.6 - - + -
196A MET* 5.1 5.6 - - + -
284A LEU* 4.3 17.5 - - + -
285A VAL 3.3 6.1 - - - +
286A LEU* 4.0 20.9 - - + -
335A SER 4.0 0.7 - - - +
336A GLU* 3.5 4.0 - - - +
337A ARG* 3.2 41.5 + - + +
348A PHE* 4.6 4.9 - - + -
349A SER* 1.3 72.8 + - - +
351A LEU* 1.3 72.2 + - - +
352A GLU* 4.8 1.3 - - + +
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Residues in contact with LEU 351 (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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283A LEU 3.6 1.0 - - - +
284A LEU* 3.3 5.9 - - - -
285A VAL* 2.8 43.8 + - + +
287A ASP* 6.2 1.8 - - + -
319A ARG* 4.8 11.7 - - + +
322A VAL* 3.6 38.6 - - + -
323A VAL* 4.3 14.1 - - + -
333A LEU* 4.1 13.7 - - + -
335A SER 3.8 2.5 - - - -
336A GLU* 3.4 31.4 - - + +
349A SER* 4.3 11.7 - - - +
350A ILE* 1.3 76.6 - - - +
352A GLU* 1.3 59.0 + - - +
353A PHE* 3.5 17.8 - - + -
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Residues in contact with GLU 352 (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* 2.7 31.5 + - + -
282A ARG* 3.4 30.3 + - - +
283A LEU 3.5 2.7 - - - -
284A LEU* 3.5 21.8 - - + -
333A LEU* 3.6 3.2 - - - +
334A ALA* 2.8 36.4 + - + +
335A SER* 2.5 50.7 + - - +
337A ARG* 4.1 4.5 + - - +
350A ILE* 5.0 2.9 - - + +
351A LEU* 1.3 74.0 - - - +
353A PHE* 1.3 56.9 + - - +
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Residues in contact with PHE 353 (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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270A LEU* 6.3 0.2 - - + -
277A LEU* 5.0 0.2 - - - +
282A ARG* 3.5 9.5 - - - -
283A LEU* 2.9 52.5 + - + +
285A VAL* 3.9 15.7 - - + -
322A VAL* 4.3 8.1 - - + -
323A VAL* 4.3 15.5 - - + -
326A ALA* 3.4 32.1 - - + -
331A LEU* 3.9 25.4 - - + -
332A ALA 3.2 23.8 - - - +
333A LEU* 3.7 21.3 - - + -
334A ALA* 4.7 0.2 - - - -
351A LEU* 3.5 35.2 - - + -
352A GLU* 1.3 75.4 - - - +
354A THR* 1.3 62.3 + - - +
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Residues in contact with THR 354 (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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277A LEU* 5.0 0.2 - - - -
280A GLY* 5.6 1.6 - - - -
281A GLY 4.0 7.0 - - - +
282A ARG* 3.3 46.7 - - - +
331A LEU* 3.4 10.2 - - - +
332A ALA* 3.0 40.0 + - - +
333A LEU 5.2 0.5 + - - -
334A ALA* 4.4 10.9 - - + +
353A PHE* 1.3 72.5 - - - +
355A ALA* 1.3 68.8 + - - +
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Residues in contact with ALA 355 (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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274A VAL* 5.0 11.2 - - + -
277A LEU* 4.4 18.4 - - + +
280A GLY 6.2 1.8 - - - +
281A GLY 4.7 0.8 + - - -
330A GLY 3.7 10.1 - - - +
331A LEU* 4.1 4.8 - - - +
354A THR* 1.3 82.7 + - - +
356A VAL* 1.3 64.1 + - - +
357A SER* 4.0 23.0 - - - +
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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