Contacts of the strand formed by residues 275 - 279 (chain B) in PDB entry 3RL7
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 CYS 275 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B TYR* 5.4 0.7 - - - -
250B ASP* 4.5 0.9 - - - -
252B SER* 4.2 18.4 - - - -
253B ILE 3.3 10.5 - - - +
254B PHE* 4.4 7.0 - - - -
273B ASN 4.0 9.2 - - - -
274B ASP* 1.3 75.8 - - - +
276B ILE* 1.3 62.3 + - - +
277B LEU* 3.6 3.8 + - + +
307B VAL* 2.9 6.9 - - - -
308B LYS* 2.8 75.0 + - + +
309B ARG* 6.2 0.2 - - - -
310B ARG* 4.0 16.8 - - - -
246D HIS* 4.5 5.2 - - - -
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Residues in contact with ILE 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B PHE* 3.9 20.9 - - + -
238B ILE* 3.9 12.1 - - + -
252B SER* 5.4 1.4 - - - -
253B ILE* 3.0 32.6 + - + +
255B ILE* 3.7 32.1 - - + -
270B LEU* 5.5 0.2 - - + -
274B ASP 4.9 0.2 - - - +
275B CYS* 1.3 71.0 - - - +
277B LEU* 1.3 63.5 + - - +
278B ARG 3.9 11.2 - - - +
279B VAL* 3.9 26.2 - - + -
284B VAL* 3.5 18.4 - - + +
285B ARG* 5.1 0.7 - - - -
296B LEU* 4.4 6.5 - - + -
305B LEU* 4.2 13.9 - - + -
306B TYR 3.7 5.6 - - - +
307B VAL* 4.3 11.4 - - + -
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASP* 6.0 2.5 - - - +
285A ARG* 6.0 0.7 - - - +
222B TYR* 3.7 35.9 - - + -
252B SER* 5.0 6.5 - - - +
275B CYS* 4.1 9.6 - - + +
276B ILE* 1.3 76.6 - - - +
278B ARG* 1.3 58.7 + - + +
283B ASP* 3.1 24.3 - - - +
284B VAL* 3.1 12.9 + - - +
285B ARG* 3.5 28.2 - - + +
306B TYR* 2.6 23.7 + - + +
307B VAL 4.4 2.2 - - - +
308B LYS* 3.8 32.1 - - + -
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Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR* 3.4 71.3 - - - +
276B ILE* 3.6 2.5 - - - +
277B LEU* 1.3 82.5 - - + +
279B VAL* 1.3 68.6 + - - +
280B ASN 2.9 31.4 + - - +
281B GLU* 3.8 8.3 + - - -
282B VAL 3.4 14.1 - - - +
283B ASP* 4.8 2.9 - - - +
284B VAL* 3.8 2.0 - - - +
304B ARG 3.4 4.0 - - - +
305B LEU* 3.8 2.3 - - - -
306B TYR* 3.1 78.2 + - + -
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Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 3.9 15.0 - - + -
278B ARG* 1.3 75.9 - - - +
280B ASN* 1.3 62.5 + - - +
281B GLU 3.1 0.7 + - - -
282B VAL* 2.8 41.0 + - - +
284B VAL* 4.3 15.9 - - + -
292B ALA* 5.2 0.7 - - + +
295B ALA* 3.7 31.4 - - + +
296B LEU* 3.9 28.5 - - + -
299B ALA* 3.9 6.3 - - + -
303B VAL* 3.7 25.1 - - + -
304B ARG 3.6 2.2 - - - -
305B LEU* 4.3 1.3 - - + -
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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
------------------------------------------------------------
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