Contacts of the strand formed by residues 335 - 341 (chain B) in PDB entry 2C11
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 TRP 335 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330B VAL 4.7 0.4 - - - -
331B ALA* 4.7 0.2 - - - -
332B SER* 2.9 41.0 + - - +
334B LEU* 1.3 88.2 - - + +
336B THR* 1.3 65.3 + - - +
337B PHE* 4.5 8.1 - - + -
352B VAL* 3.8 20.4 - - + -
353B ARG 3.4 5.4 - - - -
354B PHE* 3.5 34.8 - + + -
359B LEU* 3.7 13.5 - - + -
460B LEU* 4.5 12.1 - - + -
479B PHE* 3.4 41.4 + + + +
480B HIS 3.0 31.1 + - - -
483B GLY* 3.3 37.0 - - - -
484B ALA 3.7 5.8 - - - -
485B ILE* 3.6 15.3 - - + -
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Residues in contact with THR 336 (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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329B ARG* 3.2 15.7 + - - -
330B VAL 3.3 6.5 - - - -
331B ALA* 3.5 24.9 - - + -
332B SER 4.4 4.3 - - - +
335B TRP* 1.3 83.3 - - - +
337B PHE* 1.3 65.7 + - - +
351B ASP 3.2 1.4 - - - +
352B VAL* 3.5 0.7 - - - +
353B ARG* 2.9 54.5 + - - +
356B GLY* 5.0 3.5 + - - -
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Residues in contact with PHE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ARG* 3.1 14.2 - - - +
330B VAL* 2.8 68.3 + - + -
335B TRP* 4.5 3.4 - - + -
336B THR* 1.3 81.8 - - - +
338B SER* 1.3 69.4 + - - +
339B PHE* 4.1 7.6 - + + -
349B ILE* 3.8 15.9 - - + -
350B PHE 3.7 4.7 - - - +
351B ASP 3.3 15.3 - - - +
352B VAL* 4.1 5.8 - - + -
460B LEU* 4.1 14.4 - - + -
462B VAL* 3.4 30.7 - - + -
479B PHE* 3.3 41.1 - + - -
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Residues in contact with SER 338 (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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58B GLN* 4.5 4.8 + - - +
60B PHE* 3.6 33.2 + - - +
328B SER* 3.2 26.2 - - - -
329B ARG* 3.6 18.9 - - - +
337B PHE* 1.3 76.5 - - - +
339B PHE* 1.3 61.8 + - - +
349B ILE* 3.2 9.0 - - - +
350B PHE* 3.1 33.5 + - - -
351B ASP* 5.7 0.9 - - - -
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Residues in contact with PHE 339 (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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60B PHE 4.0 6.7 - - - +
62B ASP* 3.8 5.2 - - - +
325B VAL* 3.7 15.0 - - + -
327B GLY 3.7 16.4 - - - -
328B SER* 2.8 44.8 + - - -
330B VAL* 3.3 31.4 - - + -
337B PHE* 4.1 8.7 - + + -
338B SER* 1.3 74.8 - - - +
340B GLY* 1.3 65.0 + - - +
348B ARG* 3.5 10.5 - - - +
349B ILE* 4.1 12.3 - - + +
350B PHE* 5.4 2.5 - - - -
411B VAL* 3.9 18.2 - - + -
429B PHE* 4.0 34.1 - + + -
431B VAL* 4.3 10.3 - - + -
462B VAL* 4.7 9.4 - - + -
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Residues in contact with GLY 340 (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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60B PHE 5.4 0.2 - - - -
62B ASP* 3.1 15.9 - - - -
339B PHE* 1.3 79.4 - - - +
341B LEU* 1.3 62.8 + - - +
347B PRO* 3.6 2.4 - - - +
348B ARG* 3.0 35.1 + - - +
429B PHE* 3.2 23.0 - - - -
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Residues in contact with LEU 341 (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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62B ASP* 2.7 25.1 + - - +
100B GLU* 3.8 1.0 - - - +
340B GLY* 1.3 73.2 - - - -
342B GLY* 1.3 63.5 + - - +
343B ALA 3.5 0.7 + - - -
346B GLY 3.8 2.2 - - - -
347B PRO* 3.4 39.7 - - + -
348B ARG* 3.1 6.6 + - - +
392B GLY* 3.6 15.0 - - - -
395B THR* 3.3 29.4 - - + +
413B TRP* 3.5 47.6 - - + +
428B ALA* 4.8 0.2 - - + -
429B PHE* 3.5 17.9 - - + -
464B SER* 3.6 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