Contacts of the strand formed by residues 452 - 456 (chain b) in PDB entry 6QX2
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 GLN 452 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421b CYS* 3.5 5.4 - - - +
430b GLU* 3.0 30.9 + - - +
432b PHE* 3.6 23.5 - - + -
447b ARG* 2.8 52.0 + - + +
448b ASP* 2.8 39.8 + - - +
451b THR* 1.3 85.5 - - - +
453b ALA* 1.3 53.6 - - - +
592b TRP* 3.4 10.5 - - - -
596b MET* 2.8 32.0 + - - +
598b PRO* 4.7 3.2 - - - +
601b ARG* 3.5 1.8 - - - +
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Residues in contact with ALA 453 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418b LEU* 4.8 1.1 - - + -
419b ALA 3.3 12.3 - - - +
420b ASP* 3.8 11.2 - - - +
421b CYS* 3.9 4.5 - - - +
430b GLU 2.8 7.9 + - - +
431b ILE* 3.5 7.7 - - + -
432b PHE* 2.9 26.6 + - - -
447b ARG* 3.9 0.7 - - - +
452b GLN* 1.3 73.4 - - - +
454b ILE* 1.3 67.1 + - - +
500b TYR* 3.5 39.0 - - + +
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Residues in contact with ILE 454 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418b LEU* 3.5 6.5 - - - +
419b ALA 2.8 37.6 + - - +
431b ILE* 4.7 0.2 - - - -
432b PHE* 3.4 10.3 - - + +
434b VAL* 4.0 25.1 - - + -
440b GLY 4.4 5.2 - - - +
443b THR* 3.4 31.6 - - + +
444b LYS* 3.5 43.7 - - + +
447b ARG* 3.5 31.6 - - + +
452b GLN 5.0 0.2 - - - +
453b ALA* 1.3 78.3 - - - +
455b LEU* 1.3 61.1 + - - +
456b PRO* 3.7 5.6 - - + +
596b MET* 4.9 1.8 - - + -
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Residues in contact with LEU 455 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417b LYS 4.6 0.4 - - - -
418b LEU* 3.9 26.5 - - + +
431b ILE* 4.1 5.1 - - + +
432b PHE 2.9 8.6 + - - -
433b LEU* 3.5 23.2 - - + +
434b VAL* 3.3 19.6 + - - -
454b ILE* 1.3 71.0 - - - +
456b PRO* 1.3 77.5 - - + +
457b LEU* 3.5 11.1 + - + +
480b GLN* 3.7 31.4 - - + +
481b MET* 3.7 44.4 - - + +
484b ALA* 4.3 9.0 - - + -
485b PHE* 5.7 0.2 - - + -
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Residues in contact with PRO 456 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417b LYS* 2.9 48.1 - - + +
434b VAL* 3.6 15.5 - - + +
436b GLY 3.8 27.4 - - - +
437b ASP* 4.5 9.0 - - - +
440b GLY* 4.3 4.0 - - - -
444b LYS* 3.6 19.7 - - - +
454b ILE* 3.7 6.1 - - + +
455b LEU* 1.3 88.5 - - + +
457b LEU* 1.3 62.9 + - - +
477b GLU* 5.0 2.9 - - - +
480b GLN* 5.2 0.7 - - - +
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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