Contacts of the strand formed by residues 440 - 450 (chain B) in PDB entry 3R2W
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 ASP 440 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396B ASN* 3.4 25.4 + - - +
438B ILE 4.0 0.2 + - - -
439B PRO* 1.3 74.2 - - - +
441B MET* 1.3 88.7 + - - +
442B LEU* 4.0 6.8 - - - +
458B ASN* 5.9 0.8 - - - +
459B VAL 2.8 7.9 + - - +
460B SER* 2.7 33.9 + - - +
461B LEU* 3.1 22.2 + - - +
462B LYS* 5.6 2.1 - - - +
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Residues in contact with MET 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B LEU* 3.6 31.0 - - + -
392B LEU* 4.4 12.8 - - + -
395B SER* 3.5 29.4 - - - +
396B ASN* 3.2 6.8 + - - +
397B LEU* 3.7 15.9 - - + -
419B VAL* 4.9 0.2 - - + -
439B PRO* 3.4 28.3 - - - +
440B ASP* 1.3 94.5 + - - +
442B LEU* 1.3 57.2 + - - +
443B GLU* 2.2 24.7 + - - +
444B LEU* 3.4 28.0 + - + -
447B LEU* 5.0 1.1 - - + -
461B LEU* 3.1 28.1 - - - +
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Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ASN* 3.4 48.7 - - - +
397B LEU* 4.0 13.0 - - + +
408B SER* 5.4 4.7 - - - +
410B LYS* 3.7 25.4 - - + +
411B ARG* 2.7 40.9 + - + +
412B GLU 5.3 1.0 + - - -
440B ASP* 4.0 6.3 - - - +
441B MET* 1.3 73.2 - - - +
443B GLU* 1.3 59.5 + - + +
444B LEU 3.2 4.2 - - - +
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Residues in contact with GLU 443 (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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411B ARG* 4.2 1.3 - - - +
412B GLU* 5.6 5.2 - - - +
441B MET 2.2 20.2 + - - +
442B LEU* 1.3 72.3 - - + +
444B LEU* 1.3 54.7 + - - -
445B ASP* 4.6 1.6 - - - +
462B LYS* 3.2 47.4 + - + +
463B GLY* 2.7 28.0 + - - -
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LEU* 4.9 0.2 - - + -
411B ARG* 3.3 26.4 + - - +
417B PRO* 3.5 18.4 - - + +
419B VAL* 4.2 11.7 - - + -
441B MET* 3.4 40.8 + - + -
442B LEU 3.2 3.6 - - - -
443B GLU* 1.3 77.2 - - - +
445B ASP* 1.3 62.7 + - - +
446B HIS 4.2 8.1 - - - +
447B LEU* 3.7 27.1 - - + +
461B LEU* 3.6 39.5 - - + +
462B LYS 3.8 0.9 - - - +
463B GLY 3.7 13.7 - - - +
465B VAL* 5.0 3.1 - - + -
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Residues in contact with ASP 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ARG* 5.1 1.2 + - - -
415B THR* 4.5 19.4 + - - +
416B VAL 4.9 0.5 - - - +
417B PRO* 3.8 4.4 - - - +
418B LEU* 3.4 27.1 + - - +
443B GLU 4.6 1.3 - - - +
444B LEU* 1.3 77.7 - - - +
446B HIS* 1.3 59.2 + - - +
463B GLY* 2.8 27.4 + - - +
464B THR* 3.8 12.3 - - + +
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Residues in contact with HIS 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LEU* 3.4 41.7 - - + +
420B LYS* 3.7 16.4 + - - +
444B LEU* 4.2 5.5 - - - +
445B ASP* 1.3 77.2 - - - +
447B LEU* 1.3 81.9 + - - +
448B THR* 3.5 35.4 - - + +
463B GLY 3.3 4.0 + - - +
464B THR* 3.3 25.9 - - + +
465B VAL 3.1 21.7 + - - -
466B ILE* 5.4 3.8 - - + -
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Residues in contact with LEU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B LEU* 4.3 14.1 - - + -
418B LEU 3.0 7.3 + - - +
419B VAL* 3.4 26.2 - - + -
420B LYS 3.0 25.4 + - - +
421B LEU* 4.9 3.6 - - + -
435B PHE* 5.7 5.2 - - + -
441B MET* 5.0 0.2 - - + -
444B LEU* 3.7 17.7 - - + +
446B HIS* 1.3 75.9 - - - +
448B THR* 1.3 62.5 + - - +
449B VAL* 4.0 22.9 - - + -
455B PHE* 5.4 1.6 - - + -
461B LEU* 3.8 28.7 - - + -
465B VAL* 3.4 32.5 - - + +
467B ILE* 4.9 0.9 - - + -
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Residues in contact with THR 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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420B LYS* 3.5 32.0 + - - +
446B HIS* 3.5 24.0 - - + +
447B LEU* 1.3 75.4 - - - +
449B VAL* 1.3 61.2 + - - +
450B SER* 4.2 0.9 + - - -
465B VAL 3.1 4.5 + - - +
466B ILE* 3.5 35.7 - - + +
467B ILE 2.8 31.9 + - - +
468B ILE* 6.0 0.4 - - - -
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Residues in contact with VAL 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LYS* 3.4 5.7 + - - +
421B LEU* 3.4 24.9 - - + -
422B GLY* 2.8 29.0 + - - -
425B PHE* 3.5 26.5 - - + -
447B LEU* 4.0 21.5 - - + -
448B THR* 1.3 82.0 + - - +
450B SER* 1.3 60.1 + - - +
453B VAL* 3.6 27.6 - - + -
455B PHE* 4.2 9.2 - - + -
467B ILE* 3.4 20.9 - - + +
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Residues in contact with SER 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B GLY* 4.1 13.7 - - - -
448B THR* 4.2 0.9 - - - -
449B VAL* 1.3 75.6 - - - +
451B GLY* 1.3 63.7 + - - +
453B VAL* 4.2 2.1 - - - +
467B ILE 3.1 9.7 + - - +
468B ILE* 3.4 22.9 - - - +
469B ALA 3.1 22.8 + - - -
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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