Contacts of the strand formed by residues 417 - 423 (chain A) in PDB entry 3QTC
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 TRP 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A LEU* 6.0 0.2 - - + -
348A TRP* 3.2 29.6 - + + +
349A GLN 3.1 18.6 - - - +
350A MET* 4.0 7.0 - - + -
354A CYS* 3.6 6.7 - - - +
401A LEU* 3.6 36.8 - - + -
402A VAL* 3.5 1.1 - - - +
403A GLY* 2.7 47.6 + - - +
404A PRO* 4.4 0.2 - - + -
405A ILE* 3.9 13.7 - - + -
408A ASP* 2.9 35.8 + - - -
413A ILE* 4.4 9.4 - - + +
415A LYS 3.5 20.9 - - - -
416A PRO* 1.3 75.4 - - - +
418A ILE* 1.3 71.7 + - - +
811A 0A1 3.7 18.8 - - - -
812A EDO 3.6 29.4 - - - -
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Residues in contact with ILE 418 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A PHE* 5.1 1.6 - - + -
348A TRP* 3.5 2.8 - - - -
349A GLN* 2.9 47.2 + - + +
353A GLY 4.2 13.2 - - - +
354A CYS* 3.6 17.9 - - - +
355A THR 3.6 21.8 - - - +
358A ASN* 4.2 6.5 - - + -
359A LEU* 3.8 35.7 - - + +
362A ILE* 4.2 14.6 - - + -
401A LEU 3.4 5.6 - - - +
402A VAL* 4.0 16.4 - - + -
417A TRP* 1.3 85.3 - - - +
419A GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 419 (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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347A PHE* 3.1 17.0 - - - -
359A LEU* 3.7 9.3 - - - +
400A ALA* 3.4 2.8 - - - +
401A LEU 3.0 30.5 + - - +
417A TRP* 3.9 1.6 - - - -
418A ILE* 1.3 77.4 - - - +
420A ALA* 1.3 64.2 + - - +
811A 0A1 3.2 17.0 - - - -
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Residues in contact with ALA 420 (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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345A LEU 3.8 0.3 - - - +
346A VAL* 3.2 4.5 - - - +
347A PHE* 3.1 56.9 + - + +
363A ILE* 4.5 2.5 - - + -
398A SER* 3.7 10.5 - - - +
399A SER 3.4 6.1 - - - -
400A ALA* 3.6 18.6 - - + -
419A GLY* 1.3 76.6 - - - +
421A GLY* 1.3 60.5 + - - +
422A PHE* 4.1 5.5 - - + -
811A 0A1 3.4 9.4 + - - -
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Residues in contact with GLY 421 (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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344A MET* 4.2 2.7 - - - -
345A LEU 3.1 8.7 - - - -
346A VAL* 3.9 11.0 - - - -
398A SER* 2.9 25.8 + - - -
399A SER 3.0 13.3 + - - -
420A ALA* 1.3 75.5 - - - +
422A PHE* 1.3 60.8 + - - -
810A ANP 3.6 11.0 - - - +
811A 0A1 3.8 14.2 - - - -
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Residues in contact with PHE 422 (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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344A MET* 3.3 7.4 - - - +
345A LEU* 2.8 60.1 + - + +
347A PHE* 4.0 22.7 - + - -
363A ILE* 4.2 24.5 - - + -
366A PHE* 4.1 19.5 - + - -
367A LEU* 3.8 26.7 - - + -
390A VAL* 4.6 1.1 - - + -
397A LEU* 3.5 14.4 - - + -
398A SER* 3.5 30.3 - - - -
420A ALA* 4.1 7.2 - - + -
421A GLY* 1.3 75.3 - - - -
423A GLY* 1.3 61.2 + - - +
424A LEU 3.6 0.2 + - - -
427A LEU* 4.1 26.7 - - + -
810A ANP 4.2 0.4 - - - -
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Residues in contact with GLY 423 (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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343A THR 3.5 7.9 - - - -
344A MET* 4.6 0.7 - - - -
397A LEU 3.5 2.1 + - - +
422A PHE* 1.3 72.0 - - - +
424A LEU* 1.3 64.1 + - - -
425A GLU 3.3 3.4 - - - -
426A ARG* 3.3 7.2 + - - +
427A LEU* 3.1 24.7 + - - +
810A ANP 3.0 41.4 + - - -
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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