Contacts of the strand formed by residues 442 - 448 (chain A) in PDB entry 6Q6Q
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 ASN 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A HIS* 4.5 4.0 - - + -
365A ASP* 3.8 6.8 + - - -
366A SER 2.6 30.5 + - - +
367A ASP* 2.8 23.5 + - - +
370A PRO* 4.3 4.3 - - + +
428A PHE 3.2 15.0 - - - +
429A ARG* 3.8 13.9 - - + -
439A ALA* 4.0 6.7 - - + +
441A VAL* 1.3 75.6 - - - +
443A SER* 1.3 66.3 + - - +
463A TYR* 3.6 6.2 - - - -
464A GLY* 3.0 41.1 + - - +
522A PHE* 4.2 0.9 - - - -
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Residues in contact with SER 443 (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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340A HIS* 4.0 2.3 - - - -
370A PRO* 4.2 8.9 - - - +
371A ILE* 4.7 0.5 - - - +
426A SER 4.9 0.2 - - - -
427A ALA* 3.3 6.5 - - - +
428A PHE* 2.8 33.8 + - - +
442A ASN* 1.3 78.9 - - - +
444A GLY* 1.3 61.5 + - - +
445A MET* 3.2 29.4 - - - +
462A SER 2.4 23.5 + - - -
463A TYR* 3.4 17.6 - - - -
522A PHE* 4.2 10.5 - - - -
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Residues in contact with GLY 444 (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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370A PRO* 3.9 19.3 - - - +
371A ILE* 4.5 7.4 - - - -
374A VAL* 3.2 15.8 - - - +
425A VAL* 5.8 0.2 - - - -
426A SER 3.6 7.0 - - - -
427A ALA* 4.3 3.1 - - - -
443A SER* 1.3 75.8 + - - +
445A MET* 1.3 62.5 + - - +
462A SER* 2.9 28.0 + - - -
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Residues in contact with MET 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A VAL* 4.1 1.6 - - - +
425A VAL* 3.1 4.5 - - - +
426A SER 2.9 36.1 + - - +
428A PHE* 4.5 5.4 - - + -
443A SER* 3.2 22.4 - - - +
444A GLY* 1.3 79.5 - - - +
446A ARG* 1.3 59.4 - - - +
460A CYS 3.6 4.0 - - - -
461A ILE* 3.6 20.4 - - + -
463A TYR* 3.3 26.9 - - + +
522A PHE* 3.9 25.8 - - + +
523A LEU* 3.9 13.0 - - + +
526A PHE* 3.6 47.5 - - + -
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Residues in contact with ARG 446 (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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333A MET* 6.1 1.1 - - - -
374A VAL* 2.5 34.6 + - + +
375A GLY* 3.8 10.9 - - - -
376A ASN* 3.4 24.1 + - - +
420A ARG* 3.8 1.4 - - - +
423A GLU* 2.7 41.0 + - + +
424A PHE 3.5 9.6 - - - +
425A VAL* 3.7 18.6 - - + -
445A MET* 1.3 74.7 - - - +
447A VAL* 1.3 67.8 + - - +
448A PHE* 4.3 4.4 - - - +
458A GLU* 3.0 37.8 + - - +
459A LEU* 3.5 6.9 - - - +
460A CYS* 2.9 48.4 + - - +
526A PHE* 4.4 0.9 - - - -
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Residues in contact with VAL 447 (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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422A TRP 4.2 0.2 - - - +
423A GLU* 3.6 4.0 - - - +
424A PHE* 2.9 40.4 + - + +
446A ARG* 1.3 77.4 - - - +
448A PHE* 1.3 65.7 + - - +
449A PHE* 3.8 20.6 - - + -
456A ILE* 4.3 7.4 - - + -
458A GLU 3.7 7.6 - - - +
459A LEU* 3.7 21.5 - - + -
485A TRP* 3.9 20.4 - - + -
526A PHE* 4.0 13.9 - - + -
530A VAL* 3.8 28.5 - - + -
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Residues in contact with PHE 448 (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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420A ARG* 3.7 39.0 - - + -
421A LYS 3.5 22.0 - - - -
422A TRP 3.4 13.9 - - - -
423A GLU* 3.5 19.3 - - + -
446A ARG* 4.3 1.8 - - - +
447A VAL* 1.3 76.5 - - - +
449A PHE* 1.3 62.8 + - - +
450A GLY* 3.7 21.5 - - - -
456A ILE* 3.6 2.9 - - - -
457A ARG* 2.8 33.1 + - + -
458A GLU* 3.0 51.2 + - + +
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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