Contacts of the strand formed by residues 249 - 254 (chain C) in PDB entry 2J9F
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 MET 249 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.8 19.7 - - + +
23A ILE 3.5 4.7 - - - +
24A GLN* 3.6 44.9 - - + +
25A PRO* 4.2 6.7 - - + -
247C GLY 4.0 1.4 + - - +
248C ILE* 1.3 69.9 - - - +
250C SER* 1.3 57.6 + - - +
271C ARG* 3.6 33.9 - - - +
277C GLN* 3.5 26.9 - - - +
278C PRO 3.8 3.1 + - - +
279C PHE* 3.4 30.3 - - + -
280C LEU 2.9 23.4 + - - +
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Residues in contact with SER 250 (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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22A PHE* 3.4 3.3 - - - -
23A ILE* 2.6 44.9 + - - +
31C ILE* 5.6 0.4 - - - -
240C ALA* 3.5 22.9 - - - -
243C GLY* 3.2 18.9 - - - -
244C PRO* 3.6 6.4 - - - +
248C ILE 2.7 18.1 + - - -
249C MET* 1.3 74.0 + - - +
251C ILE* 1.3 63.9 + - - +
280C LEU* 3.2 16.8 - - - +
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Residues in contact with ILE 251 (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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20A LEU* 3.8 33.0 - - + -
21A GLU 3.7 25.6 - - - +
22A PHE* 3.5 24.7 - - + -
23A ILE* 5.1 5.2 - - + -
31C ILE* 6.1 0.2 - - + -
32C PRO 5.8 0.2 - - - +
34C TYR* 4.6 8.5 - - + -
240C ALA* 4.2 6.1 - - - +
250C SER* 1.3 78.2 - - - +
252C ARG* 1.3 69.7 + - - +
253C VAL* 4.2 7.2 - - + -
264C ALA* 4.1 16.8 - - + -
280C LEU 2.9 6.3 + - - +
281C ILE* 3.4 20.9 - - + -
282C GLU* 2.9 26.3 + - - +
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Residues in contact with ARG 252 (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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12A ALA* 3.4 16.9 - - - +
14A ALA* 4.3 2.2 - - - +
30C GLY 4.2 0.4 - - - -
31C ILE* 2.9 42.8 + - + +
32C PRO 3.4 11.7 + - - +
33C ILE* 3.6 20.0 - - + -
34C TYR* 2.9 27.4 + - - +
237C ASP* 2.7 54.0 + - - -
238C GLY* 3.7 4.2 - - - +
240C ALA* 3.9 11.9 - - + +
251C ILE* 1.3 76.9 - - - +
253C VAL* 1.3 65.5 + - - +
282C GLU* 2.8 32.8 + - - +
284C MET* 3.6 24.5 - - + -
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Residues in contact with VAL 253 (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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33C ILE* 3.6 5.6 - - - -
34C TYR* 3.5 22.2 - - + +
251C ILE* 4.2 10.5 - - + -
252C ARG* 1.3 79.7 - - - +
254C ASP* 1.3 60.1 + - - +
255C GLY 3.2 0.7 + - - -
260C ALA* 4.2 6.7 - - + +
261C VAL* 4.0 22.0 - - + -
264C ALA* 3.5 30.3 - - + -
281C ILE* 4.1 10.8 - - + -
282C GLU 3.0 8.5 + - - +
283C ALA* 3.8 23.3 - - + -
284C MET* 2.9 31.0 + - - +
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Residues in contact with ASP 254 (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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9A PHE* 3.2 23.3 - - - -
16A PHE* 3.9 14.8 - - - -
33C ILE* 3.4 13.5 - - + +
34C TYR 2.8 19.4 + - - +
35C ARG* 4.2 9.5 - - + +
253C VAL* 1.3 69.5 - - - +
255C GLY* 1.3 58.4 + - - +
256C ASN* 2.9 19.5 + - - +
257C ASP* 3.1 30.3 + - + +
260C ALA* 4.1 1.7 - - - +
261C VAL* 3.7 4.2 - - - +
284C MET 4.2 1.6 - - - -
318C ARG* 2.9 32.7 + - - -
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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