Contacts of the strand formed by residues 274 - 278 (chain C) in PDB entry 3C6Q
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 ASP 274 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C PRO* 5.5 1.9 - - - +
97C ARG* 2.9 40.6 + - - -
98C TYR 4.2 2.4 - - - +
266C LYS* 3.3 6.2 - - - +
267C VAL* 2.7 51.6 + - + +
272C LYS* 5.0 7.9 - - - +
273C VAL* 1.3 76.1 - - - +
275C TYR* 1.3 86.5 + - - +
276C VAL* 4.4 5.0 - - - +
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Residues in contact with TYR 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ARG* 4.2 0.3 + - - -
98C TYR 3.8 19.5 - - - +
99C VAL* 3.8 16.9 - - + -
100C TYR 3.4 12.1 + - - -
261C LEU* 3.8 58.1 - - + +
262C MET* 4.5 12.5 - - - +
264C LEU* 4.6 2.9 - - + -
265C PRO 3.6 16.8 - - - +
266C LYS* 4.2 23.8 + - + -
273C VAL* 4.2 20.6 - - + +
274C ASP* 1.3 99.8 + - - +
276C VAL* 1.3 72.5 + - - +
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Residues in contact with VAL 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ASP* 5.5 0.9 - - - +
97C ARG* 5.0 0.4 - - - +
99C VAL* 3.9 1.9 - - - +
100C TYR* 3.3 38.4 - - + +
264C LEU* 5.5 0.2 - - - +
265C PRO* 3.4 31.0 + - - +
267C VAL* 4.5 21.6 - - + +
274C ASP* 4.4 11.8 + - - +
275C TYR* 1.3 85.4 - - - +
277C ILE* 1.3 65.6 + - - +
278C ASP* 3.8 16.3 + - + +
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Residues in contact with ILE 277 (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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262B MET 3.7 21.8 - - - +
263B MET* 4.0 35.4 - - + +
99C VAL* 4.0 10.5 - - + -
100C TYR 2.7 12.7 + - - +
101C ILE* 3.7 19.6 - - + -
102C GLY 3.2 19.1 + - - -
244C LEU* 4.1 15.9 - - + -
248C VAL* 4.1 18.6 - - + -
264C LEU* 4.3 8.7 - - + -
265C PRO* 4.4 11.0 - - + -
276C VAL* 1.3 76.3 - - - +
278C ASP* 1.3 68.6 + - - +
279C THR* 3.1 7.2 + - + +
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Residues in contact with ASP 278 (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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262B MET 5.1 2.6 - - - +
102C GLY 3.4 7.3 - - - +
104C ASP* 3.9 33.7 + - - +
265C PRO* 5.6 1.2 - - - +
276C VAL* 3.8 12.6 + - + +
277C ILE* 1.3 75.2 - - - +
279C THR* 1.3 62.3 + - - +
280C GLY* 3.0 20.8 + - - -
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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