Contacts of the strand formed by residues 258 - 263 (chain B) in PDB entry 5E5R
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 GLN 258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B SER* 4.6 12.2 + - - -
256B VAL 3.8 1.5 + - - +
257B PRO* 1.3 76.4 - - - +
259B ILE* 1.3 71.8 + - - +
260B ASN* 3.5 17.2 + - - +
278B PHE 5.0 2.8 + - - -
279B ASN* 3.5 30.1 - - - +
298B ILE 3.4 4.9 - - - +
300B GLU* 2.8 34.8 + - + +
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Residues in contact with ILE 259 (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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249B CYS* 3.7 24.7 - - - +
250B PHE* 4.4 16.8 - - + -
251B ALA* 4.5 5.8 - - + +
257B PRO* 5.0 5.8 - - + +
258B GLN* 1.3 79.4 + - - +
260B ASN* 1.3 66.9 + - - +
261B TRP* 3.7 12.7 - - - +
278B PHE 5.1 2.2 - - - +
279B ASN* 2.8 59.9 + - + +
280B GLY* 4.7 1.8 - - - -
297B CYS* 3.8 20.2 - - - -
298B ILE 3.3 2.0 - - - +
299B ALA* 3.7 25.4 - - + -
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Residues in contact with ASN 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLN* 3.5 23.5 + - - +
259B ILE* 1.3 78.3 - - - +
261B TRP* 1.3 68.6 + - - +
279B ASN* 5.0 2.3 + - - +
297B CYS* 3.6 3.5 - - - -
298B ILE* 2.7 53.2 + - + +
300B GLU* 3.8 22.8 + - - +
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Residues in contact with TRP 261 (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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233B PHE* 3.7 24.9 - + - -
247B LEU* 3.6 46.2 - - + -
249B CYS* 3.5 32.8 - - + -
259B ILE* 3.7 8.2 - - + +
260B ASN* 1.3 83.0 - - - +
262B ARG* 1.3 68.4 + - - +
269B PHE* 3.9 19.1 - - + -
275B LEU* 3.3 29.2 - - + +
279B ASN 2.9 23.3 + - - -
280B GLY 4.1 3.6 - - - -
281B MET 4.3 1.4 + - - -
282B LEU* 3.7 27.4 - - + -
295B TYR* 5.2 3.1 - + + -
296B GLU 3.5 18.6 - - - -
297B CYS* 3.9 4.3 - - + -
298B ILE* 5.1 0.2 - - - +
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Residues in contact with ARG 262 (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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261B TRP* 1.3 78.6 - - - +
263B ARG* 1.3 70.4 + - - +
269B PHE* 3.5 17.0 - - - -
295B TYR* 3.8 2.3 - - - -
296B GLU* 2.8 58.7 + - + +
298B ILE* 3.3 32.5 - - + +
305B LYS* 5.5 8.5 - - - +
307B VAL* 5.6 2.6 - - - +
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Residues in contact with ARG 263 (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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262B ARG* 1.3 89.8 - - - +
264B SER* 1.3 65.3 + - - +
265B ASP* 2.8 40.9 + - - +
266B GLY* 3.6 9.3 + - - +
267B MET* 3.3 33.2 + - - +
268B PRO 4.6 3.8 - - - -
269B PHE* 3.4 29.4 - - + +
270B PRO* 5.7 2.5 - - - -
290B GLU 4.4 6.9 + - - -
291B ASP* 4.0 4.6 + - - +
292B THR 3.1 28.3 + - - -
293B GLY* 3.8 12.7 - - - -
294B SER 3.6 8.6 - - - +
295B TYR* 3.8 24.5 + - + +
296B GLU 5.0 0.4 - - - -
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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