Contacts of the strand formed by residues 335 - 342 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C ALA* 3.3 2.4 - - - -
332C SER* 2.7 44.8 + - - +
334C LEU* 1.3 89.2 - - + +
336C THR* 1.3 63.9 + - - +
337C PHE* 4.6 5.6 - - + -
352C VAL* 3.6 26.5 - - + -
353C ARG 3.6 8.3 - - - -
354C PHE* 3.4 30.3 - + + -
359C LEU* 3.8 16.4 - - + -
460C LEU* 4.5 16.2 - - + -
479C PHE* 3.2 48.3 - + + +
480C HIS 3.1 34.4 + - - -
483C GLY* 3.6 16.2 - - - -
484C ALA 3.9 1.6 - - - -
485C ILE* 3.5 20.9 - - + -
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Residues in contact with THR 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C ARG* 2.7 30.1 - - - +
330C VAL 3.7 7.4 - - - +
331C ALA* 3.9 12.6 - - - +
332C SER 5.0 0.9 + - - -
335C TRP* 1.3 78.0 + - - +
337C PHE* 1.3 67.4 + - - +
351C ASP 3.1 0.3 - - - +
352C VAL* 3.2 1.6 - - - +
353C ARG* 2.7 65.5 + - + +
356C GLY* 5.7 1.6 - - - -
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Residues in contact with PHE 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C ARG* 3.1 12.7 - - - +
330C VAL* 3.0 67.0 + - + +
335C TRP* 4.6 1.6 - - + -
336C THR* 1.3 88.2 - - - +
338C SER* 1.3 69.4 + - - +
339C PHE* 4.1 10.5 - + - -
349C ILE* 3.7 20.0 - - + -
350C PHE 3.6 4.0 - - - +
351C ASP 3.0 15.5 - - - +
352C VAL* 3.9 14.1 - - + -
460C LEU* 4.3 10.8 - - + -
462C VAL* 3.3 33.9 - - + -
479C PHE* 3.8 30.5 - + - -
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Residues in contact with SER 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLN* 5.3 1.7 + - - +
60C PHE* 3.3 30.2 - - - +
61C ALA 4.3 0.9 + - - -
328C SER* 3.1 15.6 + - - -
329C ARG* 3.6 24.1 - - - +
337C PHE* 1.3 78.2 - - - +
339C PHE* 1.3 66.4 + - - +
349C ILE* 3.1 4.7 - - - +
350C PHE* 2.6 47.0 + - - +
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Residues in contact with PHE 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C PHE* 4.6 6.1 - - - +
61C ALA* 4.8 0.2 - - - -
325C VAL* 4.3 5.4 - - + -
327C GLY 3.8 16.8 - - - -
328C SER* 2.7 60.2 + - - -
330C VAL* 3.6 29.6 - - + -
337C PHE* 4.1 7.2 - + + -
338C SER* 1.3 77.2 + - - +
340C GLY* 1.3 62.9 + - - +
348C ARG* 3.3 11.2 - - - +
349C ILE* 3.9 12.8 - - + -
350C PHE* 5.6 2.5 - - - -
411C VAL* 4.0 23.8 - - + -
429C PHE* 3.8 42.4 - + + -
431C VAL* 4.4 5.6 - - + -
462C VAL* 4.3 13.5 - - + -
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Residues in contact with GLY 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C PHE 5.5 0.7 - - - -
62C ASP* 3.4 18.2 - - - -
328C SER* 5.2 0.4 - - - -
339C PHE* 1.3 85.7 - - - +
341C LEU* 1.3 62.9 + - - +
347C PRO* 3.6 2.9 - - - +
348C ARG* 2.9 34.4 + - - +
429C PHE* 3.5 13.0 - - - -
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Residues in contact with LEU 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ASP* 3.0 15.2 + - - +
100C GLU* 3.9 2.3 - - - +
340C GLY* 1.3 74.2 - - - +
342C GLY* 1.3 63.3 + - - +
343C ALA 3.8 0.2 + - - -
346C GLY* 3.3 4.3 - - - -
347C PRO* 3.3 39.5 - - + -
348C ARG* 3.8 7.8 + - - +
391C MET 5.0 1.8 - - - +
392C GLY* 3.4 29.8 - - - +
395C THR* 3.5 28.9 - - + +
413C TRP* 3.3 35.9 + - + +
428C ALA* 5.3 0.9 - - + -
429C PHE* 3.5 19.7 - - + -
464C SER* 3.8 11.4 - - - +
466C SER* 5.4 0.2 - - - +
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Residues in contact with GLY 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLU* 3.3 12.8 - - - -
341C LEU* 1.3 73.5 - - - +
343C ALA* 1.3 63.8 + - - -
344C PHE 3.3 2.7 - - - -
345C SER* 4.1 8.1 - - - -
346C GLY 2.6 30.8 + - - -
348C ARG* 3.4 13.5 - - - +
392C GLY* 2.9 21.8 - - - -
413C TRP* 4.6 0.2 - - - -
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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