Contacts of the strand formed by residues 281 - 287 (chain C) in PDB entry 5C5B
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 ALA 281 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279C ARG* 6.3 0.7 - - + -
280C LYS* 1.3 86.6 + - - +
282C GLY* 1.3 58.5 + - - +
301C PHE* 3.5 22.2 - - + -
302C TYR 3.3 5.8 - - - -
303C PHE* 3.5 13.9 - - + -
366C TRP* 4.1 4.3 - - - -
14D GLN* 4.5 12.1 + - - +
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Residues in contact with GLY 282 (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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280C LYS* 5.8 0.7 - - - -
281C ALA* 1.3 75.8 - - - +
283C TYR* 1.3 60.5 + - - -
301C PHE* 3.5 18.2 - - - -
302C TYR* 2.7 41.7 + - - +
362C ASP* 6.2 0.2 - - - -
366C TRP* 3.8 11.4 - - - -
14D GLN* 5.6 0.7 - - - -
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Residues in contact with TYR 283 (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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282C GLY* 1.3 72.2 - - - -
284C LEU* 1.3 71.0 + - - +
299C ARG* 3.2 53.6 - - + +
300C GLN* 3.3 19.5 - - - -
301C PHE* 3.6 33.4 - + + -
314C ARG* 3.6 28.8 + - + +
356C GLN 4.7 0.2 - - - +
357C ALA* 5.1 1.4 - - - -
358C GLU* 5.3 5.0 + - - +
362C ASP* 5.7 1.2 - - - +
366C TRP* 5.2 0.2 + - - -
14D GLN 3.7 13.2 - - - -
15D ASP* 2.6 31.5 + - + -
17D PRO* 3.3 15.4 - - - +
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Residues in contact with LEU 284 (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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282C GLY 3.8 2.0 + - - +
283C TYR* 1.3 84.1 - - - +
285C ASN* 1.3 69.8 + - - +
298C ASP 3.6 1.4 - - - +
299C ARG* 3.5 2.1 - - - -
300C GLN 2.9 30.9 + - - +
302C TYR* 3.7 30.3 - - + -
309C LEU* 5.9 0.4 - - + -
342C PHE* 3.9 22.0 - - + -
355C LEU* 4.2 11.7 - - + -
356C GLN 3.5 18.6 - - - +
357C ALA* 3.6 16.4 - - + -
362C ASP* 5.7 0.7 - - + -
366C TRP* 3.4 47.1 - - + +
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Residues in contact with ASN 285 (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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284C LEU* 1.3 74.1 - - - +
286C ALA* 1.3 60.2 + - - +
297C TRP* 3.9 20.9 - - + +
298C ASP 3.5 4.2 - - - +
299C ARG* 3.3 34.7 + - - +
354C ILE 3.5 1.0 - - - +
355C LEU* 3.2 6.7 - - - +
356C GLN* 2.5 71.3 + - + +
357C ALA 5.4 1.6 + - - -
148D SER* 3.7 17.0 + - - -
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Residues in contact with ALA 286 (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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285C ASN* 1.3 74.8 - - - +
287C ARG* 1.3 63.2 + - - +
288C ASN* 3.4 12.8 + - - +
296C THR 3.5 0.2 - - - +
297C TRP* 3.2 6.8 - - - -
298C ASP* 3.1 37.1 + - + +
300C GLN* 6.5 0.7 - - + -
302C TYR* 3.3 26.0 - - - +
353C SER* 4.0 10.8 - - - -
354C ILE 3.4 3.8 - - - -
355C LEU* 3.8 9.0 - - + -
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Residues in contact with ARG 287 (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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286C ALA* 1.3 69.5 - - - +
288C ASN* 1.3 67.4 + - - +
295C SER* 5.8 2.0 - - - +
296C THR 3.4 5.8 - - - -
297C TRP* 3.6 36.9 - - + +
335C CYS* 5.0 2.5 - - - -
336C GLU* 5.4 2.5 - - - +
353C SER* 3.8 11.8 + - - -
354C ILE* 3.1 30.1 + - + +
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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