Contacts of the strand formed by residues 447 - 453 (chain B) in PDB entry 6QNW
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 PHE 447 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B ILE* 3.9 24.0 - - + -
303B THR* 4.3 0.3 - - - +
304B GLY* 2.9 40.7 + - - +
305B ASP 3.9 8.7 - - - -
306B ASN* 3.1 39.9 - - - -
424B LEU* 5.7 3.1 - - + -
441B LEU 3.4 9.9 - - - +
442B GLN* 3.3 28.9 - - - +
445B ASP 3.3 5.9 + - - -
446B ASP* 1.3 75.4 - - - +
448B ALA* 1.3 64.5 + - - +
449B LEU* 4.4 8.5 - - + -
466B PHE* 3.9 23.3 - + - -
470B CYS* 6.0 0.7 - - - -
475B ILE* 5.4 1.8 - - + -
477B MET* 3.5 24.9 - - + -
491B GLU 5.0 1.8 - - - +
492B PHE* 4.0 3.1 - - - -
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Residues in contact with ALA 448 (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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301B THR* 5.5 1.1 - - + -
302B ILE 3.6 7.0 - - - +
304B GLY 4.8 0.2 - - - +
424B LEU* 5.3 0.7 - - - +
440B GLY* 3.1 4.0 - - - -
441B LEU* 2.9 39.6 + - + +
447B PHE* 1.3 73.5 - - - +
449B LEU* 1.3 60.7 + - - +
450B ILE* 4.5 4.9 - - + +
490B PHE* 3.8 33.4 - - + -
491B GLU 4.1 3.8 - - - +
492B PHE* 3.7 20.3 - - + -
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Residues in contact with LEU 449 (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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301B THR* 3.2 8.5 - - - +
302B ILE* 2.9 55.6 + - + +
424B LEU* 3.8 11.7 - - + -
438B TRP* 3.6 33.4 - - + -
439B ASP 3.3 24.2 - - - +
447B PHE* 4.2 7.2 - - + -
448B ALA* 1.3 73.2 - - - +
450B ILE* 1.3 68.1 + - - +
451B VAL* 4.3 10.1 - - + +
463B VAL* 5.8 4.9 - - + -
466B PHE* 3.5 39.0 - - + -
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Residues in contact with ILE 450 (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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285B VAL* 3.7 25.8 - - + -
286B VAL* 4.8 16.8 - - + +
289B MET* 3.5 34.5 - - + +
300B PHE 3.5 3.8 - - - +
301B THR* 3.5 17.5 - - + +
438B TRP* 3.3 1.4 - - - -
439B ASP 2.9 41.3 + - - +
440B GLY* 4.3 4.9 - - - -
441B LEU* 5.2 3.8 - - + -
448B ALA* 4.5 5.2 - - + +
449B LEU* 1.3 82.4 - - - +
451B VAL* 1.3 62.0 + - - +
452B ASN* 4.0 4.7 - - - +
487B THR* 3.5 26.9 - - + +
490B PHE* 5.6 5.4 - - + -
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Residues in contact with VAL 451 (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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298B LEU 3.6 1.6 - - - +
299B SER* 3.5 0.2 - - - -
300B PHE* 2.9 38.2 + - + +
302B ILE* 5.0 7.6 - - + -
436B TYR* 4.7 8.7 - - + -
437B TRP 3.5 14.6 - - - +
438B TRP* 3.8 15.7 - - + +
449B LEU* 4.9 7.4 - - + -
450B ILE* 1.3 74.1 - - - +
452B ASN* 1.3 74.8 + - - +
459B ILE* 4.0 26.1 - - + +
462B GLY* 4.9 8.7 - - - -
463B VAL* 4.2 22.4 - - + +
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Residues in contact with ASN 452 (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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289B MET* 3.2 48.5 + - - +
292B ASN* 4.7 3.4 - - - +
297B GLU* 5.2 5.0 - - + +
298B LEU 3.3 8.3 - - - +
299B SER* 2.9 31.2 + - - +
436B TYR* 3.3 3.1 - - - +
437B TRP* 2.9 61.4 + - + +
450B ILE* 4.0 2.4 - - - +
451B VAL* 1.3 82.5 - - - +
453B ALA* 1.3 61.7 + - - +
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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
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296B THR 4.7 0.4 - - - -
297B GLU* 4.1 1.1 - - - -
298B LEU* 3.2 29.4 + - - +
435B THR 4.5 0.7 - - - -
436B TYR* 4.0 13.2 - - + +
437B TRP* 5.3 0.4 - - - -
451B VAL* 5.3 0.2 - - + -
452B ASN* 1.3 76.4 - - - +
454B PRO* 1.3 77.6 - - + +
455B ASN 3.3 3.3 + - - +
458B GLY* 3.9 7.2 - - - -
459B ILE* 3.5 35.9 - - + +
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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