Contacts of the strand formed by residues 434 - 440 (chain A) in PDB entry 4QQN
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 CYS 434 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A SER* 3.2 3.5 - - - -
384A LEU* 2.9 31.4 + - + +
432A GLU 3.9 0.2 + - - -
433A PRO* 1.3 74.8 - - - +
435A GLY* 1.3 76.9 + - - +
436A ILE* 3.5 4.4 + - + +
454A ASP 5.4 1.1 - - - -
455A PHE* 4.0 21.8 - - + -
456A THR* 3.5 29.8 - - - +
457A LEU* 3.7 13.0 - - + -
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Residues in contact with GLY 435 (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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381A THR* 5.9 3.1 - - - -
382A ILE 3.4 10.1 - - - -
383A SER* 3.8 8.1 + - - -
433A PRO 4.3 0.2 - - - -
434A CYS* 1.3 84.1 - - - +
436A ILE* 1.3 60.0 + - - +
437A LYS 3.6 2.2 - - - -
453A SER* 4.6 2.1 + - - -
454A ASP 5.5 0.7 - - - +
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Residues in contact with ILE 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A PHE* 4.2 9.0 - - + -
382A ILE* 2.8 41.1 + - + +
383A SER 4.4 0.7 - - - +
384A LEU* 3.9 34.1 - - + -
434A CYS 3.8 9.2 - - - +
435A GLY* 1.3 78.6 - - - +
437A LYS* 1.3 62.8 + - + +
451A PHE* 3.4 20.1 - - + -
453A SER* 3.4 35.7 - - - +
455A PHE* 4.1 14.4 - - + -
520A VAL* 3.8 24.7 - - + -
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Residues in contact with LYS 437 (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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353A LEU* 5.8 0.2 - - - -
381A THR* 3.1 9.7 - - - +
382A ILE* 3.0 46.3 + - + +
435A GLY* 3.6 2.1 - - - -
436A ILE* 1.3 82.0 - - - +
438A HIS* 1.3 70.1 + - - +
439A ILE* 3.9 29.4 - - + -
448A ASP* 2.7 38.2 + - - +
449A LEU* 4.9 1.3 - - - +
451A PHE* 3.7 46.9 - - + +
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Residues in contact with HIS 438 (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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379A ILE* 3.5 30.2 - - + +
380A CYS 3.5 4.0 - - - -
381A THR* 4.0 19.7 - - + -
437A LYS* 1.3 82.5 + - - +
439A ILE* 1.3 72.0 + - - +
440A ASP* 4.2 12.4 + - + -
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Residues in contact with ILE 439 (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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352A LEU* 3.9 26.7 - - + -
353A LEU* 4.5 5.6 - - + -
358A LEU* 4.5 12.1 - - + -
379A ILE* 3.3 6.6 - - - +
380A CYS* 2.8 43.9 + - + +
437A LYS* 3.9 28.5 - - + -
438A HIS* 1.3 81.5 + - - +
440A ASP* 1.3 60.1 + - - +
441A CYS* 4.1 22.9 - - - -
444A THR* 3.5 24.9 - - + +
449A LEU* 4.1 20.0 - - + -
610A UNX 4.6 0.7 - - - -
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Residues in contact with ASP 440 (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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378A ASP* 3.3 9.9 - - - +
379A ILE* 3.9 16.7 - - - +
438A HIS* 4.2 15.5 + - + -
439A ILE* 1.3 70.7 - - - +
441A CYS* 1.3 58.5 + - - +
442A HIS* 3.0 35.6 + - - +
443A THR* 3.1 19.3 + - - +
444A THR* 2.6 34.8 + - - -
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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