Contacts of the strand formed by residues 249 - 256 (chain C) in PDB entry 4BVH
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 GLY 249 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C ASN 4.1 11.6 - - - +
230C ILE* 4.2 4.9 - - - +
246C GLU* 2.9 28.0 + - - +
247C ALA 3.4 1.0 + - - -
248C HIS* 1.3 81.7 - - - +
250C THR* 1.3 65.6 + - - -
290C ASP 3.2 11.7 - - - -
291C ILE* 4.2 2.2 - - - -
292C VAL* 3.9 5.3 - - - +
299C PRO* 4.2 5.6 - - - +
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Residues in contact with THR 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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230C ILE 5.0 3.8 - - - -
232C GLY* 5.8 3.6 - - - -
246C GLU* 3.5 25.6 + - + +
249C GLY* 1.3 77.9 - - - -
251C PHE* 1.4 55.9 + - - +
252C ALA* 3.0 29.1 + - + +
253C SER* 3.4 19.6 - - - +
290C ASP* 2.9 34.8 + - + +
291C ILE* 3.6 10.9 - - - +
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Residues in contact with PHE 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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192C PHE* 4.1 12.1 - + - -
195C LEU* 5.5 1.1 - - + -
196C ALA* 3.6 32.5 - - + -
199C LEU* 3.9 29.8 - - + -
200C TYR* 3.6 37.2 + + + -
201C PRO* 4.6 13.2 - - + -
230C ILE* 3.4 52.8 + - + -
231C ASP* 5.3 0.7 - - - -
250C THR* 1.4 68.9 + - - +
252C ALA* 1.3 62.9 + - - +
253C SER 3.1 7.2 + - - +
265C GLY* 3.4 14.9 - - - -
289C PRO* 3.6 27.1 - - + -
291C ILE* 4.2 5.2 - - + -
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Residues in contact with ALA 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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235C ARG* 3.5 31.0 - - - +
246C GLU* 5.7 0.7 - - - +
250C THR* 3.0 20.9 + - + +
251C PHE* 1.3 77.2 - - - +
253C SER* 1.3 56.5 + - - +
264C PRO* 3.7 4.2 - - - +
265C GLY* 2.7 23.2 + - - -
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Residues in contact with SER 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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250C THR* 3.4 15.1 + - - +
251C PHE 3.1 2.8 - - - +
252C ALA* 1.3 82.5 - - - +
254C ALA* 1.3 63.0 + - - +
262C PRO* 6.4 0.7 - - - -
263C PHE 3.4 13.0 - - - -
264C PRO* 4.7 1.3 - - - -
265C GLY* 3.6 4.5 - - - +
289C PRO* 3.7 2.6 - - - +
290C ASP* 2.5 47.2 + - - +
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Residues in contact with ALA 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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253C SER* 1.3 75.8 - - - +
255C THR* 1.3 67.5 + - - +
262C PRO* 3.4 2.6 - - - +
263C PHE* 2.7 46.1 + - + +
265C GLY* 4.5 4.5 - - - +
268C ILE* 4.1 16.2 - - + -
287C VAL* 3.7 20.9 - - + -
288C LYS 3.3 17.3 - - - +
289C PRO* 3.9 3.8 - - + -
290C ASP* 3.4 4.3 - - - +
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Residues in contact with THR 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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254C ALA* 1.3 74.8 + - - +
256C CYS* 1.3 77.8 + - - +
257C THR* 3.2 1.7 + - - +
260C GLN* 3.6 33.2 - - + +
261C ARG 3.4 5.2 - - - +
262C PRO* 4.5 6.1 - - + +
263C PHE* 4.6 0.2 - - - -
287C VAL* 4.1 2.7 - - - -
288C LYS* 2.9 33.5 + - - +
290C ASP* 2.6 26.0 + - - -
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Residues in contact with CYS 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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255C THR* 1.3 72.2 - - - +
257C THR* 1.3 59.4 + - - +
258C VAL 3.1 17.5 - - - -
259C CYS* 3.5 10.3 - - - -
260C GLN* 3.0 30.3 + - - -
261C ARG 2.9 17.4 + - - +
263C PHE* 4.0 6.3 - - + -
280C CYS* 3.4 18.2 - - + -
283C CYS* 3.4 9.4 - - - -
285C GLY* 3.9 9.4 - - - -
286C VAL 3.8 4.7 - - - -
287C VAL* 4.1 4.5 - - - +
1400C ZN 2.4 36.6 - - - -
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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