Contacts of the strand formed by residues 244 - 251 (chain A) in PDB entry 1Q0P
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 MET 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A SER* 1.3 77.7 + - - +
245A ASN* 1.3 74.9 + - - +
246A ILE* 4.0 27.4 - - + -
275A VAL* 5.9 1.3 - - - -
280A VAL* 6.4 1.3 - - - -
281A LYS 5.7 0.4 + - - -
282A PRO* 3.2 18.6 - - + +
283A ARG* 3.0 23.9 + - - +
355A THR* 4.4 0.2 - - - -
356A ARG* 3.2 59.7 - - + +
358A VAL* 4.0 9.4 - - + -
451A SER 4.2 12.3 - - - +
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Residues in contact with ASN 245 (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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243A SER* 5.0 0.5 + - - -
244A MET* 1.3 80.4 + - - +
246A ILE* 1.3 63.8 + - - +
247A TYR* 3.0 35.4 + - + +
283A ARG* 3.3 43.8 + - - +
299A VAL* 4.0 15.6 - - + +
340A MET 5.6 0.4 + - - -
355A THR* 3.9 12.0 - - - +
356A ARG 2.9 6.1 + - - +
357A HIS* 3.6 14.8 - - - +
358A VAL 2.8 26.5 + - - -
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Residues in contact with ILE 246 (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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244A MET* 4.0 14.4 - - - -
245A ASN* 1.3 77.1 - - - +
247A TYR* 1.3 62.4 + - - +
248A LEU* 3.7 13.7 - - + -
271A LEU* 5.3 0.7 - - + -
275A VAL* 4.5 5.2 - - + -
282A PRO* 3.8 29.4 - - + -
283A ARG 2.9 8.0 + - - +
284A TYR* 3.3 30.3 - - + +
285A GLY 2.8 25.3 + - - +
299A VAL* 4.8 0.2 - - - +
358A VAL* 3.3 11.0 - - + +
360A ILE* 3.6 28.3 - - + -
451A SER* 3.6 24.9 - - - -
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Residues in contact with TYR 247 (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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245A ASN* 3.0 34.1 + - + -
246A ILE* 1.3 72.1 - - - +
248A LEU* 1.3 60.3 + - - +
249A VAL* 3.7 3.0 + - + +
285A GLY* 3.8 4.7 - - - -
287A VAL* 6.5 0.4 - - + -
299A VAL* 3.8 21.7 - - + +
337A VAL* 3.8 33.7 - - + -
340A MET* 3.9 33.2 - - + -
341A MET* 3.6 23.0 - - + +
357A HIS* 2.7 36.8 + - + -
358A VAL 2.7 23.7 + - - +
359A ILE* 3.6 11.2 - - + -
360A ILE 2.8 31.8 + - - +
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Residues in contact with LEU 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 ILE* 3.7 22.7 - - + -
247A TYR* 1.3 69.4 - - - +
249A VAL* 1.3 62.2 + - - +
250A LEU 4.1 0.4 - - - -
268A LEU* 4.1 29.4 - - + -
271A LEU* 4.4 4.7 - - + -
272A ILE* 3.9 28.0 - - + -
284A TYR* 4.0 15.9 - - + -
285A GLY 2.9 16.6 + - - +
286A LEU* 3.4 23.4 - - + +
287A VAL* 2.8 27.8 + - - +
310A VAL* 4.8 6.3 - - + -
314A LEU* 4.9 2.9 - - + -
360A ILE* 3.7 20.2 - - + -
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Residues in contact with VAL 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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247A TYR* 4.0 10.5 - - + +
248A LEU* 1.3 77.3 - - - +
250A LEU* 1.3 60.7 + - - +
251A ASP 4.1 0.2 - - - -
268A LEU* 5.5 0.4 - - - +
287A VAL* 3.3 14.1 - - + +
289A TYR* 3.8 19.3 - - + -
333A ALA* 4.0 14.8 - - + +
334A LEU* 5.2 2.0 - - + -
337A VAL* 3.7 29.4 - - + -
359A ILE* 4.4 9.0 - - + -
360A ILE 2.9 10.3 + - - +
361A LEU* 3.4 26.7 - - + +
362A MET* 2.9 29.1 + - - +
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Residues in contact with LEU 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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248A LEU 4.1 0.6 - - - -
249A VAL* 1.3 74.0 - - - +
251A ASP* 1.3 74.1 + - - +
252A GLY 3.3 0.7 + - - -
256A ILE* 6.0 1.1 - - + -
261A PHE* 3.5 35.7 - - + -
264A ALA* 3.5 27.6 - - + -
265A LYS* 3.8 26.5 - - + +
268A LEU* 4.5 17.5 - - + -
286A LEU* 5.7 3.6 - - + -
287A VAL 2.8 13.2 + - - +
288A THR* 3.1 31.8 - - + -
289A TYR* 3.1 5.6 + - - -
314A LEU* 5.0 4.0 - - + -
317A ILE* 5.7 0.4 - - + -
362A MET* 3.6 17.7 - - + +
405A VAL* 5.6 1.1 - - + -
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Residues in contact with ASP 251 (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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250A LEU* 1.3 74.3 - - - +
252A GLY* 1.3 57.5 + - - +
253A SER* 2.7 33.1 + - - -
256A ILE* 3.5 24.6 - - + +
261A PHE* 3.6 14.8 - - - -
289A TYR* 3.4 30.6 + - + +
328A THR* 3.6 12.5 - - - +
362A MET 3.0 22.2 + - - +
363A THR* 2.8 24.8 + - - -
364A ASP* 3.9 3.5 - - - +
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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