Contacts of the strand formed by residues 252 - 259 (chain B) in PDB entry 4R54
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 HIS 252 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B CYS* 3.3 31.0 - - + -
129B SER* 3.5 25.4 - - - +
132B GLN* 3.1 30.5 + - - +
154B TYR 3.7 4.9 - - - +
155B GLN* 3.4 21.5 + - + -
156B ALA 3.0 36.6 + - - -
159B GLY* 4.6 2.5 - - - -
245B ARG* 4.5 2.5 - - - -
251B ALA* 1.3 72.4 - - - +
253B SER* 1.3 62.0 + - - +
254B GLU* 5.2 1.6 - - + -
322B VAL* 3.3 4.0 - - - +
323B SER 2.9 20.0 + - - +
325B ASN* 3.4 31.1 + - + +
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Residues in contact with SER 253 (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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205A ALA* 4.2 7.2 - - - +
153B THR* 4.0 0.5 - - - -
154B TYR* 2.7 48.6 + - - -
251B ALA 4.7 0.2 + - - -
252B HIS* 1.3 74.6 - - - +
254B GLU* 1.3 66.4 + - - +
293B ALA* 4.1 17.0 + - - +
320B TRP* 3.3 31.9 - - - -
321B VAL 3.3 4.5 - - - -
322B VAL* 3.5 16.2 - - - +
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Residues in contact with GLU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B SER* 2.6 42.1 - - - +
132B GLN* 3.4 29.1 + - - +
133B MET* 3.6 21.0 + - - +
151B VAL* 3.9 14.8 - - + -
152B SER 3.6 4.3 - - - +
153B THR* 4.1 10.5 - - + -
154B TYR* 4.5 0.2 - - - -
224B MET* 3.8 7.7 - - - +
252B HIS* 5.1 1.7 - - + +
253B SER* 1.3 81.8 - - - +
255B SER* 1.3 60.3 + - - +
256B VAL* 3.6 7.0 + - + +
320B TRP* 3.3 12.1 - - - -
321B VAL* 2.8 40.0 + - + +
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Residues in contact with SER 255 (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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152A SER* 2.7 32.9 + - - -
242A THR* 3.5 21.4 + - - +
150B ILE 4.0 0.7 - - - +
151B VAL* 3.4 4.5 - - - +
152B SER* 2.9 36.0 + - - -
154B TYR* 4.1 8.5 - - - -
254B GLU* 1.3 70.2 - - - +
256B VAL* 1.3 61.5 + - - +
318B HIS* 5.6 2.4 + - - +
319B MET 3.6 6.1 + - - -
320B TRP* 3.8 12.7 - - - -
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B MET* 4.5 7.2 - - + -
137B LEU* 4.2 21.1 - - + -
149B ILE* 4.3 9.2 - - + -
150B ILE 3.9 2.2 - - - -
151B VAL* 4.1 8.3 - - + -
254B GLU* 3.9 27.8 - - + +
255B SER* 1.3 77.0 + - - +
257B TYR* 1.3 65.3 + - - +
258B ILE* 3.9 23.1 - - + +
317B ILE 3.9 0.5 - - - +
318B HIS* 3.3 5.5 - - - +
319B MET* 2.9 43.8 + - + +
321B VAL* 3.9 18.8 - - + -
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Residues in contact with TYR 257 (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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148A ARG* 2.9 18.1 + - - -
150A ILE* 3.6 26.0 - - + -
148B ARG* 4.9 5.6 - - + -
149B ILE* 3.3 4.7 - - - +
150B ILE* 2.8 59.0 + - + +
255B SER 4.2 0.2 + - - -
256B VAL* 1.3 72.6 - - - +
258B ILE* 1.3 71.2 - - - +
259B GLU* 2.6 46.9 + - + +
310B ASP* 3.5 17.5 - - + -
313B ALA* 3.5 9.5 - - - +
316B GLY* 3.5 9.0 - - - -
317B ILE 3.4 11.0 - - - -
318B HIS* 3.3 29.6 - + + +
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Residues in contact with ILE 258 (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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137B LEU* 3.6 41.1 - - + -
140B VAL* 3.9 28.7 - - + -
146B LEU* 4.0 14.8 - - + -
148B ARG 3.3 7.2 - - - +
149B ILE* 4.1 9.6 - - + -
256B VAL* 3.9 6.5 - - + -
257B TYR* 1.3 84.1 - - - +
259B GLU* 1.3 62.0 + - - +
260B THR* 4.1 8.7 - - + -
315B LYS 3.7 0.2 - - - +
316B GLY* 3.2 4.5 - - - -
317B ILE* 2.8 56.8 + - + +
319B MET* 4.2 9.9 - - + -
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Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 2.9 21.0 + - - -
146B LEU* 3.7 2.2 - - - -
147B ASP* 2.7 42.7 + - + +
148B ARG* 3.0 38.8 + - + +
257B TYR* 2.6 36.6 + - + +
258B ILE* 1.3 74.7 - - - +
260B THR* 1.3 59.3 + - - +
313B ALA* 4.0 6.1 - - + +
315B LYS* 3.3 8.7 - - + +
316B GLY* 3.7 11.0 - - - +
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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