Contacts of the strand formed by residues 245 - 249 (chain A) in PDB entry 4BOS
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 ARG 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A VAL* 3.6 0.9 - - - +
240A ASP* 2.8 43.1 + - + +
243A THR* 3.8 18.2 - - - +
244A VAL* 1.3 74.6 - - - +
246A ILE* 1.3 73.2 + - - +
247A ASP* 3.1 27.3 + - - +
298A LEU* 4.3 2.2 - - - -
301A ALA* 5.4 1.1 - - - +
11C LYS* 6.1 1.4 - - - +
34C GLU* 2.5 28.7 + - - +
35C GLY 3.0 19.6 - - - -
36C ILE* 3.2 27.3 - - - +
37C PRO* 4.2 9.2 - - - -
40C GLN* 4.5 6.8 + - - -
71C LEU* 5.4 0.2 - - - +
8E LEU 3.4 13.0 - - - +
9E THR* 2.9 32.9 + - - +
10E GLY* 4.2 0.7 - - - -
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Residues in contact with ILE 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A CYS* 3.9 19.1 - - + -
238A VAL 3.3 9.4 - - - +
239A VAL* 4.2 18.8 - - + -
245A ARG* 1.3 86.1 + - - +
247A ASP* 1.3 66.6 + - - +
248A ARG* 3.8 27.9 + - + +
294A LEU* 3.6 36.8 - - + +
297A ALA* 4.4 1.8 - - + -
298A LEU* 4.3 15.3 - - + +
8E LEU* 2.9 41.5 + - + +
9E THR* 5.3 2.3 - - - +
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Residues in contact with ASP 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE 3.5 4.5 - - - +
238A VAL* 2.9 41.0 + - + +
240A ASP* 4.3 13.6 - - - +
245A ARG* 3.1 35.7 + - - +
246A ILE* 1.3 72.8 - - - +
248A ARG* 1.3 60.8 - - - +
249A PHE* 3.6 21.6 + - + -
9C THR* 4.1 4.0 - - + -
40C GLN* 4.5 1.8 - - - +
71C LEU* 3.8 22.3 - - + +
73C LEU* 3.7 23.5 - - + +
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Residues in contact with ARG 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLU* 3.1 22.2 + - - +
236A ILE 3.9 2.9 - - - -
237A CYS* 4.1 8.9 - - - +
246A ILE* 3.8 26.1 + - + +
247A ASP* 1.3 72.4 - - - +
249A PHE* 1.3 61.4 + - - +
251A GLU* 3.2 53.3 + - + +
258A ARG* 2.9 31.1 - - - +
291A ASP* 4.7 1.4 + - - -
294A LEU* 4.0 21.3 - - - +
9C THR* 3.4 14.1 - - - +
8E LEU* 4.3 12.4 - - - +
70E VAL* 4.4 0.8 - - - +
71E LEU* 3.2 38.6 + - - +
72E ARG* 5.5 1.0 - - - +
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Residues in contact with PHE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ALA* 3.7 30.1 - - + -
225A ILE* 3.6 27.1 - - + -
226A SER* 3.9 20.4 - - - -
229A SER* 3.3 14.1 + - - -
235A GLU* 3.2 8.0 - - - +
236A ILE* 2.8 44.8 + - + +
238A VAL* 4.3 5.6 - - + -
247A ASP* 3.8 10.8 - - + -
248A ARG* 1.3 71.0 - - - +
250A GLY* 1.3 57.8 + - - +
8C LEU* 4.0 4.3 - - + -
9C THR* 3.7 34.8 - - + -
71C LEU* 4.9 0.2 - - + -
73C LEU* 3.9 23.8 - - + -
1078C NO3 3.8 20.0 - - - -
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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