Contacts of the strand formed by residues 245 - 251 (chain H) in PDB entry 1A7R
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 LEU 245 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237H VAL* 3.9 12.6 - - + -
238H ARG 3.4 3.8 - - - -
239H GLN* 3.9 29.8 - - + +
244H GLY* 1.3 73.8 - - - -
246H GLU* 1.3 60.1 + - - +
247H TRP 4.2 0.2 - - - -
294H TYR* 4.6 5.6 - - + -
306H TRP* 4.3 2.5 - - + -
36L TYR* 5.4 0.4 - - + -
38L GLN* 4.5 1.1 - - - +
44L PRO* 3.9 34.8 - - + -
87L TYR* 3.9 29.4 - - + -
98L PHE* 3.7 58.8 + - + +
99L GLY 4.8 2.6 - - - +
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Residues in contact with GLU 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237H VAL* 3.4 5.1 - - - +
238H ARG* 2.7 72.8 + - + +
240H PRO* 4.9 9.7 - - + +
244H GLY 4.8 2.7 - - - +
245H LEU* 1.3 74.8 - - - +
247H TRP* 1.3 72.6 + - - +
248H LEU* 3.4 5.1 + - + +
260H ASN* 3.7 8.7 + - - +
262H ALA* 5.7 1.6 - - - +
263H LEU* 3.2 23.6 - - - +
98L PHE 6.0 0.2 - - - +
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Residues in contact with TRP 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235H ASN* 2.7 25.9 + - - -
236H TRP 4.0 10.1 - - - -
237H VAL* 4.5 5.2 - - + +
246H GLU* 1.3 70.1 - - - +
248H LEU* 1.3 60.3 + - - +
249H GLY* 3.6 30.4 + - - -
250H MET* 3.9 14.4 - - + -
258H ASP* 3.9 20.2 - - + -
259H TYR 3.6 15.9 - - - -
260H ASN* 2.8 34.4 + - + +
303H LEU* 5.4 0.4 - - + -
89L GLN* 4.7 3.1 - - - -
94L THR* 4.6 0.9 - - + -
95L PRO* 3.4 28.5 - - + -
96L ARG* 3.3 64.2 - - + +
97L THR* 4.4 2.4 - - - +
98L PHE* 4.0 29.1 - + + +
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Residues in contact with LEU 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236H TRP* 2.9 22.7 + - + +
237H VAL 4.3 0.9 - - - +
238H ARG* 3.7 30.5 - - + +
246H GLU* 3.8 11.9 - - + +
247H TRP* 1.3 77.4 - - - +
249H GLY* 1.3 55.7 + - - +
259H TYR* 3.6 2.6 - - - -
260H ASN* 2.8 30.4 + - - +
263H LEU* 3.5 29.8 - - + -
267H LEU* 3.7 23.7 - - + +
269H ILE* 4.9 0.9 - - - -
280H LEU* 4.0 17.5 - - + -
282H MET* 5.5 0.4 - - + -
293H TYR* 3.8 34.5 - - + -
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Residues in contact with GLY 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235H ASN* 3.3 5.2 - - - +
236H TRP 2.7 31.9 + - - +
247H TRP* 3.6 17.2 + - - -
248H LEU* 1.3 81.0 - - - +
250H MET* 1.3 59.3 + - - +
258H ASP 3.1 13.9 - - - -
259H TYR* 4.0 0.2 - - - -
269H ILE* 3.6 14.4 - - - -
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Residues in contact with MET 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233H GLY* 4.5 12.8 - - - -
234H VAL 3.3 12.3 - - - +
235H ASN* 3.7 14.6 - - - +
236H TRP* 4.8 0.4 - - - +
247H TRP* 3.9 10.5 - - + -
249H GLY* 1.3 76.1 - - - +
251H ILE* 1.3 61.2 + - - +
252H TRP* 3.6 49.1 - - + +
257H THR* 3.2 7.3 - - - -
258H ASP* 2.9 38.6 + - + +
269H ILE* 3.6 9.4 - - - +
298H GLU* 3.2 27.4 - - - +
94L THR* 5.0 2.2 - - - -
96L ARG* 3.5 25.8 - - - -
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Residues in contact with ILE 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H TYR 4.7 0.3 - - - +
233H GLY* 3.5 1.4 - - - -
234H VAL* 3.1 35.6 + - + +
250H MET* 1.3 76.0 - - - +
252H TRP* 1.3 72.0 + - - +
255H GLY* 4.1 11.2 - - - +
256H ASN 3.3 10.5 - - - +
257H THR* 3.9 15.0 - - + -
269H ILE* 3.7 20.2 - - + +
270H SER* 4.0 17.3 - - - -
271H LYS* 3.6 35.0 - - + -
278H VAL* 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