Contacts of the strand formed by residues 341 - 345 (chain A) in PDB entry 1QO0
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 ARG 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A VAL* 3.3 6.6 - - - +
254A ALA 2.8 41.3 + - - +
255A PRO 2.9 27.3 + - - +
257A PHE* 3.7 16.0 - - + -
260A ILE* 3.2 45.9 - - - +
262A THR* 5.4 3.4 - - - +
324A GLN 2.9 28.7 + - - -
339A SER* 3.5 13.3 + - - -
340A SER* 1.3 80.4 + - - +
342A ILE* 1.3 64.5 + - - +
353A VAL* 4.1 15.8 - - + +
355A TRP* 3.3 8.3 - - - +
356A GLN* 3.4 35.6 + - + +
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Residues in contact with ILE 342 (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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130A PRO 3.7 14.4 - - - +
131A LEU* 3.7 14.8 - - + +
134A TYR* 3.4 50.7 - - + -
251A VAL* 3.7 26.2 - - + -
252A VAL 3.5 3.8 - - - +
253A VAL* 4.1 15.0 - - + -
341A ARG* 1.3 78.9 - - - +
343A ALA* 1.3 62.5 + - - +
353A VAL* 3.8 2.1 - - - -
354A ARG* 3.0 24.7 + - + +
355A TRP* 2.9 36.3 + - + +
379A MET* 4.5 0.4 - - + -
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Residues in contact with ALA 343 (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 GLN 3.6 0.7 - - - +
251A VAL* 3.1 9.8 - - - +
252A VAL* 2.8 36.9 + - + +
257A PHE* 3.8 29.5 - - + -
342A ILE* 1.3 74.5 - - - +
344A GLU* 1.3 61.4 + - - +
351A PHE* 4.1 16.2 - - + -
352A GLN 3.3 20.2 - - - +
353A VAL* 4.1 1.6 - - - -
354A ARG* 4.4 1.8 - - - +
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Residues in contact with GLU 344 (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 TYR* 4.7 3.2 + - - +
139A TYR* 4.5 12.9 + - - -
249A GLY* 4.1 26.4 - - - +
250A GLN 3.3 3.6 - - - +
251A VAL* 4.4 9.2 - - + -
343A ALA* 1.3 74.2 - - - +
345A ILE* 1.3 70.9 + - - +
352A GLN* 3.0 31.8 + - + +
354A ARG* 3.2 38.8 + - + +
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Residues in contact with ILE 345 (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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239A VAL* 4.4 13.5 - - + -
247A ALA* 3.5 26.2 - - + +
248A GLU* 4.4 0.5 - - - +
249A GLY* 2.9 25.8 + - - -
250A GLN* 2.8 49.4 + - + +
252A VAL* 4.2 11.7 - - + -
344A GLU* 1.3 76.8 - - - +
346A ASP* 1.3 75.2 + - - +
349A GLY* 3.6 24.7 - - - +
350A VAL 3.6 3.1 - - - -
351A PHE* 3.8 40.2 - - + -
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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