Contacts of the strand formed by residues 351 - 358 (chain C) in PDB entry 4LCC
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 TYR 351 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C SER* 4.6 8.8 + - - -
144C HIS* 4.1 19.9 + - - -
317C GLY 3.2 7.6 + - - -
318C PHE* 2.9 48.0 + - + +
319C TYR* 3.8 9.4 - + - -
321C PRO* 3.4 30.7 - - + +
343C ILE* 3.6 29.4 - - + -
344C LEU 3.2 7.9 - - - +
345C PRO* 3.4 29.6 - - + -
346C SER* 3.9 4.0 - - - +
349C GLY* 3.2 23.2 + - - -
350C THR* 1.3 81.8 - - - +
352C GLN* 1.3 61.7 + - - +
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Residues in contact with GLN 352 (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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10C TYR* 3.1 29.8 - - + +
11C SER 3.1 22.4 + - - +
12C ARG* 4.1 7.3 + - - +
314C ARG* 2.9 29.5 + - - +
315C ALA 3.0 20.0 - - - +
316C TYR* 3.3 28.3 - - - +
317C GLY 4.9 0.2 - - - +
318C PHE* 3.4 2.0 - - - -
344C LEU* 2.7 40.8 + - + +
346C SER* 4.3 8.9 + - - -
351C TYR* 1.3 75.9 - - - +
353C THR* 1.3 63.0 + - - +
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Residues in contact with THR 353 (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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314C ARG* 3.5 5.9 - - - -
315C ALA* 3.0 28.1 + - - +
318C PHE* 3.5 19.9 - - + -
323C ILE* 4.1 11.1 - - + +
325C ILE* 3.2 25.7 - - - +
342C GLY 3.0 25.6 - - - +
343C ILE* 3.5 15.7 - - + -
344C LEU* 5.0 0.2 - - - -
352C GLN* 1.3 78.4 - - - +
354C TRP* 1.3 74.9 + - - +
355C VAL* 5.8 0.2 - - - +
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Residues in contact with TRP 354 (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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8C GLN* 3.0 31.3 + - - -
312C TYR* 4.9 13.0 - + + -
313C CYS 3.0 17.3 - - - +
314C ARG* 3.3 44.5 - - + +
325C ILE* 4.6 1.6 - - - -
339C ASP* 3.3 44.4 - - + -
340C TYR* 4.4 0.4 - - - +
341C GLY* 3.0 44.2 + - - -
342C GLY 4.3 1.0 + - - -
344C LEU* 4.4 3.6 - - + -
353C THR* 1.3 82.3 + - - +
355C VAL* 1.3 73.7 + - - +
356C SER* 3.4 24.9 - - - -
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Residues in contact with VAL 355 (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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313C CYS* 3.1 22.1 + - - +
325C ILE* 3.3 41.2 - - + +
326C ASN* 4.3 2.5 - - - -
327C TRP* 2.7 53.8 + - + +
338C THR* 5.2 5.4 - - + -
339C ASP 3.2 9.6 - - - +
340C TYR* 4.2 15.7 - - + -
353C THR* 5.8 0.2 - - - +
354C TRP* 1.3 81.9 - - - +
356C SER* 1.3 62.2 + - - +
357C VAL* 4.9 2.0 - - + -
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Residues in contact with SER 356 (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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310C THR* 4.2 9.6 - - - +
311C LEU 3.1 12.8 - - - -
312C TYR* 4.0 19.2 - - - -
327C TRP* 3.6 0.4 - - - +
337C ASP 3.8 0.6 - - - +
338C THR* 3.2 6.1 - - - -
339C ASP* 2.9 51.1 + - - +
354C TRP* 3.4 13.3 - - - -
355C VAL* 1.3 75.0 - - - +
357C VAL* 1.3 68.9 + - - +
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Residues in contact with VAL 357 (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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310C THR* 3.6 4.2 - - - -
311C LEU* 2.9 38.0 + - + +
327C TRP* 3.3 39.4 - - + +
334C ILE* 3.8 29.2 - - + -
336C GLN 4.4 1.6 - - - +
337C ASP 3.3 7.6 - - - +
338C THR* 3.5 20.2 - - + -
355C VAL* 4.9 0.9 - - + -
356C SER* 1.3 79.4 - - - +
358C GLU* 1.3 76.6 + - - +
359C LEU* 3.7 2.0 + - - -
367C TYR* 5.6 4.3 - - + -
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Residues in contact with GLU 358 (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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309C THR 3.2 8.7 - - - +
310C THR* 4.3 10.2 - - + +
336C GLN 5.1 0.2 - - - +
337C ASP* 3.1 40.4 + - + +
357C VAL* 1.3 83.0 - - - +
359C LEU* 1.3 65.2 + - - +
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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