Contacts of the strand formed by residues 250 - 257 (chain C) in PDB entry 2HJ9
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 VAL 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235C VAL* 4.2 36.8 - - + +
238C ARG* 3.8 47.7 - - + +
248C LEU* 3.5 9.8 + - - +
249C LEU* 1.3 76.5 - - - +
251C ILE* 1.3 65.9 + - - +
252C GLU* 4.3 1.2 + - + +
267C LEU* 4.4 18.2 - - + -
268C THR 3.2 9.9 - - - +
269C VAL* 4.5 12.1 - - + -
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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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52C SER 5.2 0.4 - - - -
53C LYS* 3.9 44.9 - - + +
56C THR* 4.1 16.2 - - + +
57C SER* 4.8 2.7 - - - -
249C LEU* 4.0 26.0 - - + +
250C VAL* 1.3 77.9 - - - +
252C GLU* 1.3 70.4 + - - +
253C THR* 3.8 9.8 + - - +
266C LEU 3.3 4.7 - - - +
267C LEU* 3.3 4.0 - - - -
268C THR* 2.9 47.3 + - - +
270C GLN* 3.9 20.9 - - - +
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Residues in contact with GLU 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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57C SER* 4.1 4.3 + - - -
214C VAL* 4.9 2.6 - - - +
216C ASN 5.3 1.9 - - - +
238C ARG* 5.8 8.0 - - + +
250C VAL* 4.3 2.8 + - + -
251C ILE* 1.3 76.1 - - - +
253C THR* 1.3 61.3 + - - +
254C PRO* 3.9 7.2 - - + +
265C CYS* 3.3 34.7 - - - +
266C LEU 3.6 3.8 - - - -
267C LEU* 3.1 22.4 - - + +
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Residues in contact with THR 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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56C THR 4.8 0.2 - - - -
57C SER* 3.1 49.0 + - - +
60C ILE* 3.8 27.7 - - + +
61C HIS* 4.3 11.2 - - + -
251C ILE* 4.2 7.3 + - - +
252C GLU* 1.3 71.0 - - - +
254C PRO* 1.4 75.2 - - + +
255C ILE* 3.6 1.3 + - + +
265C CYS* 4.3 2.2 - - - +
266C LEU* 2.7 45.9 + - + +
268C THR* 5.1 2.1 + - - +
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Residues in contact with PRO 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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57C SER* 4.5 4.3 - - - +
61C HIS* 3.2 19.9 - - - -
252C GLU* 3.9 7.9 - - + +
253C THR* 1.4 88.4 - - + +
255C ILE* 1.3 62.4 + - - +
256C VAL* 3.6 6.2 + - + +
261C THR* 4.0 22.9 - - + -
264C LEU 3.7 6.7 - - - +
265C CYS* 3.8 15.0 - - - -
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Residues in contact with ILE 255 (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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60C ILE* 5.3 0.4 - - + -
61C HIS* 3.8 17.9 - - + +
64C PHE* 3.5 41.7 - - + -
213C LEU* 4.4 4.7 - - + -
253C THR* 4.2 3.8 - - + +
254C PRO* 1.3 73.0 - - - +
256C VAL* 1.3 60.3 + - - +
257C VAL* 4.1 8.5 - - + -
261C THR* 3.8 1.1 - - - +
262C THR* 2.8 40.3 + - - +
264C LEU* 2.8 43.3 + - + +
265C CYS 4.4 0.4 - - - -
266C LEU* 3.0 41.1 - - + +
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Residues in contact with VAL 256 (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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61C HIS* 2.8 36.2 + - + +
64C PHE* 4.5 2.3 - - - -
65C ASP* 4.1 5.4 - - - +
254C PRO* 4.3 7.2 - - + +
255C ILE* 1.3 75.2 - - - +
257C VAL* 1.3 65.5 + - - +
258C ASN 4.3 0.3 + - - -
259C ALA* 3.5 36.3 - - - +
260C VAL 3.5 5.2 - - - +
261C THR* 3.8 23.6 - - + +
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Residues in contact with VAL 257 (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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64C PHE* 4.7 2.7 - - + -
153C TRP* 3.5 36.1 - - + +
154C TYR 4.2 0.2 - - - -
155C TYR* 3.9 18.4 - - + +
168C LEU* 4.0 29.8 - - + -
255C ILE* 4.1 12.9 + - + -
256C VAL* 1.3 76.6 - - - +
258C ASN* 1.3 72.8 + - + +
259C ALA 3.2 0.7 - - - -
260C VAL* 2.9 22.9 + - - +
262C THR* 3.8 22.7 - - + -
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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