Contacts of the strand formed by residues 348 - 355 (chain B) in PDB entry 1XDS
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ALA* 3.4 30.1 - - + -
256B PHE* 3.7 27.8 - + + -
286B LEU* 3.9 18.6 - - + -
287B ASP 3.5 13.9 - - - +
288B ARG* 4.4 3.4 - - - +
289B ALA 5.2 0.4 - - - +
338B THR* 3.5 6.6 - - - +
339B SER* 3.1 46.1 + - - +
340B GLY 3.2 26.2 - - - -
346B PHE* 4.2 15.0 - + + -
347B ASP* 1.3 73.9 - - - +
349B SER* 1.3 74.0 + - - +
350B ILE* 4.6 3.6 - - + -
9600B DRA 3.4 27.1 - - + -
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Residues in contact with SER 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL 3.4 1.7 - - - +
286B LEU* 3.4 4.3 - - - -
287B ASP 2.9 35.7 + - - -
289B ALA* 3.7 29.4 + - - +
291B VAL* 5.7 0.3 - - - +
294B ASP* 5.4 2.1 + - - -
336B GLU* 4.6 6.9 + - - -
337B ARG 3.3 12.1 + - - -
338B THR* 4.4 6.9 + - - +
348B PHE* 1.3 79.0 + - - +
350B ILE* 1.3 65.4 + - - +
351B LEU* 4.2 14.1 - - - -
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Residues in contact with ILE 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ALA* 3.8 24.5 - - + +
174B PRO* 4.4 4.5 - - + -
177B ALA* 4.0 14.6 - - + -
178B TYR* 5.6 2.5 - - + -
284B LEU* 4.4 26.0 - - + -
285B VAL 3.4 3.6 - - - +
286B LEU* 3.4 45.8 - - + -
335B SER 4.0 0.9 - - - +
336B GLU* 3.7 2.8 - - - -
337B ARG* 3.0 50.4 + - + +
338B THR* 5.0 2.0 - - - +
339B SER* 5.2 5.2 - - - +
348B PHE* 4.6 6.1 - - + -
349B SER* 1.3 71.9 - - - +
351B LEU* 1.3 65.9 + - - +
352B GLU* 4.0 1.9 + - + +
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B LEU 3.3 4.0 - - - +
284B LEU* 4.6 1.3 - - - -
285B VAL* 3.0 40.2 + - + +
287B ASP* 6.4 0.9 - - + -
289B ALA* 4.1 20.2 - - + -
319B ARG* 4.2 18.4 - - + +
322B VAL* 4.1 27.6 - - + -
323B VAL* 5.3 1.1 - - + -
333B LEU* 4.1 9.0 - - + -
335B SER 3.7 2.2 - - - -
336B GLU* 3.3 33.2 - - + -
349B SER* 4.2 13.2 - - - -
350B ILE* 1.3 77.9 - - - +
352B GLU* 1.3 62.0 + - - +
353B PHE* 3.5 21.6 - - + -
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Residues in contact with GLU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B TYR* 2.4 39.1 + - + -
282B ARG* 3.4 36.3 + - + +
283B LEU 3.2 5.2 - - - -
284B LEU* 3.6 15.5 - - + -
333B LEU* 3.5 6.2 - - - +
334B ALA* 3.0 34.9 + - + +
335B SER* 2.7 41.8 + - - +
337B ARG* 4.1 5.6 + - - +
350B ILE* 4.0 2.1 - - + -
351B LEU* 1.3 71.4 - - - +
353B PHE* 1.3 61.3 + - - +
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Residues in contact with PHE 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B LEU* 6.0 0.2 - - + -
277B LEU* 5.0 0.2 - - - +
281B GLY 4.0 0.2 - - - +
282B ARG* 3.3 8.8 - - - +
283B LEU* 2.8 45.0 + - + +
285B VAL* 3.7 24.2 - - + -
322B VAL* 4.1 17.7 - - + -
323B VAL* 4.3 14.8 - - + -
326B ALA* 3.7 29.6 - - + -
331B LEU* 4.1 23.2 - - + +
332B ALA 3.3 20.6 - - - +
333B LEU* 3.6 22.2 - - + -
334B ALA* 4.5 0.4 - - - +
351B LEU* 3.5 33.7 - - + -
352B GLU* 1.3 73.6 - - - +
354B THR* 1.3 62.8 + - - +
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Residues in contact with THR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B LEU* 5.2 0.2 - - - -
280B GLY* 5.3 4.3 - - - +
281B GLY 3.9 9.9 - - - +
282B ARG* 4.1 24.5 - - + +
331B LEU* 3.4 9.4 - - - -
332B ALA* 3.1 39.3 + - - +
333B LEU 5.6 0.2 - - - -
334B ALA* 4.3 17.6 - - + +
353B PHE* 1.3 77.9 - - - +
355B ALA* 1.3 67.3 + - - +
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B VAL* 5.1 10.5 - - + +
277B LEU* 4.5 17.8 - - + +
280B GLY 6.4 0.4 - - - +
281B GLY 4.5 2.0 + - - -
330B GLY 3.7 7.4 - - - +
331B LEU* 4.1 5.8 - - + +
332B ALA* 5.8 0.3 - - - +
354B THR* 1.3 83.3 + - - +
356B VAL* 1.3 65.3 + - - +
357B SER 4.7 7.6 - - - +
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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