Contacts of the strand formed by residues 247 - 257 (chain A) in PDB entry 1R8E
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 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A PHE* 4.0 17.3 - - + -
240A ILE* 4.0 35.2 - - + -
245A LEU 3.9 0.8 + - - +
246A THR* 1.3 77.0 + - - +
248A VAL* 1.3 66.1 + - - +
249A SER 3.7 0.8 + - - +
274A ILE* 3.4 27.6 - - + -
275A ARG 3.3 4.5 - - - +
276A ILE* 4.4 1.8 - - + +
402A GOL 3.9 31.9 - - - +
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Residues in contact with VAL 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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246A THR* 4.2 13.5 - - - +
247A VAL* 1.3 79.6 - - - +
249A SER* 1.3 61.2 + - - +
275A ARG* 2.9 48.9 + - + +
276A ILE 4.0 9.6 - - - -
277A ALA* 4.2 12.3 - - + +
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Residues in contact with SER 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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213A PRO* 5.7 2.2 - - - -
217A TYR* 5.4 0.7 - - - -
247A VAL* 3.7 1.1 - - - +
248A VAL* 1.3 80.5 + - - +
250A ASP* 1.3 70.0 + - - +
252A TYR* 3.5 20.4 - - - -
274A ILE* 3.3 11.3 - - - +
275A ARG* 3.2 31.2 + - - -
402A GOL 2.7 28.3 + - - -
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Residues in contact with ASP 250 (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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173A THR* 3.7 15.0 + - + -
174A PHE 3.3 15.8 - - - +
175A SER* 3.6 1.9 - - - -
188A ARG* 2.8 45.5 + - - -
249A SER* 1.3 91.4 + - - +
251A VAL* 1.3 68.4 + - - +
252A TYR* 3.5 14.4 + - + +
274A ILE* 3.8 4.8 - - - +
402A GOL 2.7 33.7 + - - -
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Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A THR* 3.1 26.9 - - - -
174A PHE* 2.8 58.9 + - + +
176A PHE* 3.9 33.7 - - + -
233A LEU* 5.4 2.2 - - + -
236A LEU* 4.6 8.7 - - + -
250A ASP* 1.3 72.5 - - - +
252A TYR* 1.3 71.3 + - - +
253A GLU 4.0 0.2 + - - -
272A MET* 4.4 17.7 - - + -
273A LYS 3.6 7.9 - - - +
274A ILE* 4.0 7.0 - - + -
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Residues in contact with TYR 252 (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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134A ILE* 4.9 6.7 - - + -
136A GLN* 5.9 1.1 - - - -
172A ALA 3.8 1.6 - - - -
173A THR* 3.7 24.7 - - + -
191A PHE* 4.2 3.6 - + + -
211A THR 4.3 3.2 + - - -
212A ILE* 3.7 47.8 - - + -
213A PRO* 3.8 17.0 - - - +
217A TYR* 4.2 11.9 - + - -
249A SER* 3.5 28.9 - - - -
250A ASP* 3.5 14.6 + - + +
251A VAL* 1.3 73.7 - - - +
253A GLU* 1.3 60.9 + - - +
254A LEU* 4.2 14.0 - - + +
271A GLU 3.5 1.0 - - - +
272A MET* 3.1 7.6 - - - +
273A LYS* 2.7 47.9 + - + +
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Residues in contact with GLU 253 (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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170A TYR 3.6 0.7 - - - +
171A GLY* 3.0 6.6 - - - -
172A ALA 2.8 43.9 + - - +
174A PHE* 3.5 12.2 - - + -
187A TYR* 2.4 30.7 + - - -
191A PHE* 4.2 1.0 - - - -
229A TYR* 2.5 31.5 + - - -
252A TYR* 1.3 75.3 - - - +
254A LEU* 1.3 63.2 + - - +
255A ILE* 4.6 0.4 - - + -
270A VAL* 4.4 16.4 - - + -
271A GLU 3.4 2.5 - - - -
272A MET* 3.2 18.9 - - + +
302A IMD 2.6 22.0 + - + -
304A IMD 3.7 5.0 - - - -
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Residues in contact with LEU 254 (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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132A ILE* 5.2 12.6 - - + -
169A SER* 3.7 20.2 - - - +
170A TYR 3.4 3.8 - - - +
191A PHE* 4.0 27.4 - - + -
193A PRO* 5.3 6.3 - - + -
212A ILE* 4.7 7.2 - - + -
252A TYR* 4.4 4.0 - - + -
253A GLU* 1.3 82.7 - - - +
255A ILE* 1.3 64.2 + - - +
256A ILE* 6.0 0.7 - - - -
269A ARG 3.7 0.9 - - - +
270A VAL* 3.4 3.1 - - - -
271A GLU* 2.9 45.8 + - + +
273A LYS* 3.6 33.7 - - + -
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Residues in contact with ILE 255 (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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168A ASN 4.0 1.0 - - - +
169A SER* 3.4 4.1 - - - -
170A TYR* 2.8 44.4 + - + +
253A GLU* 4.3 1.8 - - + +
254A LEU* 1.3 80.1 - - - +
256A ILE* 1.3 63.1 + - - +
257A PRO* 4.7 0.2 - - - -
268A TYR* 3.8 32.5 - - + -
269A ARG 3.2 7.6 - - - +
270A VAL* 3.9 19.3 - - + -
302A IMD 3.3 34.3 - - + +
304A IMD 3.2 35.9 - - + +
307A IMD 5.4 6.1 - - + +
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Residues in contact with ILE 256 (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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112A MET* 5.9 8.3 - - + -
115A GLN* 4.6 14.6 - - + +
168A ASN* 3.1 39.9 - - + +
169A SER* 4.5 8.7 - - - +
254A LEU 5.8 0.4 - - - +
255A ILE* 1.3 76.7 - - - +
257A PRO* 1.3 85.6 - - + +
260A TYR* 4.4 3.4 - - - +
268A TYR* 4.3 2.7 - - - -
269A ARG* 2.8 51.5 + - + +
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Residues in contact with PRO 257 (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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168A ASN 3.6 12.3 - - - +
170A TYR* 5.3 5.6 - - + -
255A ILE 4.5 1.1 - - - +
256A ILE* 1.3 102.3 - - + +
258A ILE* 1.3 61.9 + - - +
259A HIS 3.7 15.9 - - - +
260A TYR* 3.3 41.7 - - + +
267A GLU 3.7 7.9 - - - +
268A TYR* 3.8 26.0 - - + -
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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