Contacts of the strand formed by residues 243 - 248 (chain B) in PDB entry 2R7D
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 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B GLU* 1.3 82.7 - - - +
244B ARG* 1.3 63.7 + - - +
245B VAL* 3.9 15.5 - - + -
254B VAL* 3.7 20.0 - - + -
255B PHE 3.2 9.9 - - - +
256B PRO* 3.9 5.6 - - + -
257B LEU* 3.8 10.0 - - - +
391B ARG* 3.1 25.6 + - - +
424B PRO 3.9 2.7 - - - +
425B ASP 3.5 26.9 - - - +
426B LEU* 3.7 17.7 - - - +
427B ALA* 3.7 18.6 - - + +
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Residues in contact with ARG 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASP* 5.4 3.8 - - + +
95B GLU* 3.3 39.2 + - - +
96B GLY* 4.7 3.0 - - - -
243B VAL* 1.3 71.0 - - - +
245B VAL* 1.3 63.3 + - - +
246B LYS* 2.7 37.4 - - - +
253B SER 3.6 1.4 - - - +
254B VAL* 3.2 5.9 - - - +
255B PHE* 2.5 70.2 + - + +
256B PRO 5.5 0.7 - - - -
257B LEU* 3.6 34.1 - - + +
258B PRO* 5.9 1.5 - - - +
391B ARG* 4.7 1.1 - - - +
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PRO* 3.2 39.7 - - + +
243B VAL* 3.9 13.2 - - + -
244B ARG* 1.3 74.3 - - - +
246B LYS* 1.3 61.3 + - - +
253B SER 3.5 7.2 - - - +
254B VAL* 4.5 5.8 - - + -
391B ARG* 3.6 59.0 + - + +
394B HIS* 3.9 12.3 - - + -
395B THR* 3.9 17.7 - - - +
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Residues in contact with LYS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLY* 5.1 8.7 + - - -
147B PRO* 3.3 13.4 - - - +
244B ARG* 2.7 37.9 + - + +
245B VAL* 1.3 76.9 - - - +
247B ALA* 1.3 67.3 + - - +
248B ASP* 5.1 8.5 - - + +
251B GLY 4.7 0.2 - - - -
252B ALA* 3.4 2.1 - - - +
253B SER* 2.8 39.9 + - - +
255B PHE* 3.9 20.2 - - + -
394B HIS* 4.9 0.2 - - - +
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ALA* 6.0 0.9 - - + -
147B PRO 2.9 10.9 + - - +
148B ASP* 3.3 31.9 - - + +
246B LYS* 1.3 79.5 - - - +
248B ASP* 1.3 63.7 + - - +
251B GLY 3.5 5.2 - - - +
252B ALA* 4.3 0.7 - - - -
394B HIS* 3.6 39.3 - - + +
397B ARG* 4.0 9.0 - - - +
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Residues in contact with ASP 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ALA* 5.8 3.1 - - - +
246B LYS* 5.1 9.1 - - + +
247B ALA* 1.3 76.9 - - - +
249B GLU* 1.3 62.7 + - - +
250B THR* 2.5 48.4 + - - +
251B GLY* 3.0 23.3 + - - +
397B ARG* 5.4 2.4 + - - -
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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