Contacts of the strand formed by residues 302 - 307 (chain C) in PDB entry 5Y1Z
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 GLN 302 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298C ASP* 3.2 7.8 - - - +
299C LYS 3.1 31.3 + - - +
300C ASP 4.1 5.4 - - - +
301C GLY* 1.3 80.9 - - - +
303C VAL* 1.3 67.9 + - - +
315C TRP* 3.3 45.2 + - + +
316C VAL 3.3 8.2 - - - +
317C PRO* 3.3 32.2 - - - +
318C ILE* 4.0 0.7 - - - +
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Residues in contact with VAL 303 (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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281C VAL* 5.2 0.4 - - + -
295C ALA* 4.9 11.2 - - + -
297C ARG 3.2 8.7 - - - +
298C ASP* 3.3 20.6 - - - +
302C GLN* 1.3 76.9 - - - +
304C ASP* 1.3 60.2 + - - +
305C ALA* 3.4 10.1 + - + +
315C TRP* 3.3 6.5 - - - -
316C VAL* 2.9 52.6 + - + +
318C ILE* 3.5 31.2 - - + -
321C CYS* 3.9 16.4 - - + -
369C TYR* 3.5 8.5 - - + -
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Residues in contact with ASP 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C VAL* 4.6 3.3 - - - +
294C LYS 3.3 0.7 - - - +
296C LEU* 2.9 47.7 + - - +
297C ARG* 2.9 56.4 + - + +
303C VAL* 1.3 70.6 - - - +
305C ALA* 1.3 61.7 + - - +
313C ARG* 3.8 9.3 - - - +
314C ALA* 3.8 19.9 + - - +
315C TRP* 3.5 20.1 + - + -
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Residues in contact with ALA 305 (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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281C VAL* 5.1 1.6 - - + -
283C ALA* 3.7 18.8 - - + -
293C ALA* 3.7 22.0 - - + -
294C LYS 3.1 7.4 - - - +
295C ALA* 4.8 0.4 - - - +
303C VAL* 3.4 4.4 + - + -
304C ASP* 1.3 72.3 + - - +
306C ARG* 1.3 59.2 + - - +
307C PHE* 3.8 8.2 - - + -
312C ASP 3.8 0.7 - - - +
313C ARG* 3.0 6.6 - - - -
314C ALA 2.9 38.0 + - - +
316C VAL* 4.2 9.0 - - + -
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Residues in contact with ARG 306 (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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251C GLU* 3.9 25.7 + - - -
254C VAL* 4.3 11.1 - - - +
255C CYS* 5.0 0.4 - - - +
258C CYS* 3.8 26.9 - - - +
269C TRP* 5.7 5.3 - - - -
270C PHE* 3.6 28.3 - - + -
293C ALA* 3.3 1.4 - - - -
294C LYS* 2.8 43.4 + - + +
296C LEU* 3.5 40.6 - - + +
304C ASP 3.9 0.8 + - - -
305C ALA* 1.3 69.1 - - - +
307C PHE* 1.3 63.6 + - - +
308C PHE 3.6 0.7 + - - -
311C HIS 3.6 17.5 + - - +
312C ASP 3.3 13.9 - - - +
313C ARG* 3.8 20.0 - - + +
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Residues in contact with PHE 307 (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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10A ARG* 3.8 25.6 - - - +
270C PHE* 3.7 1.7 - - - -
283C ALA* 3.6 31.0 - - + -
285C LEU* 3.9 26.9 - - + -
288C PHE* 5.6 2.9 - + - -
291C TRP* 3.7 31.9 - + + -
292C PRO 3.6 2.7 - - - -
293C ALA* 4.0 6.3 - - + -
305C ALA* 3.8 15.0 - - + -
306C ARG* 1.3 71.9 - - - +
308C PHE* 1.3 66.8 + - - +
311C HIS* 2.8 34.9 + - - +
312C ASP* 2.9 28.0 + - - +
314C ALA* 4.0 19.3 - - + -
316C VAL* 4.2 6.1 - - + -
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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