Contacts of the strand formed by residues 440 - 449 (chain B) in PDB entry 6MBZ
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 440 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373B ILE* 4.0 20.6 - - + -
374B ILE 3.4 9.9 - - - +
375B SER* 3.7 26.2 - - - -
376B GLU 4.5 1.1 - - - +
393B SER* 4.4 14.8 - - - -
424B ILE* 4.3 8.1 - - + -
426B ARG* 4.2 37.2 - - + -
427B SER* 6.0 1.1 - - - -
438B GLU* 3.9 26.0 - - + -
439B LYS* 1.3 77.1 - - - +
441B THR* 1.3 66.1 + - - +
465B PRO* 3.4 5.2 - - - +
466B VAL* 2.6 41.1 + - + +
468B VAL* 3.5 34.8 - - + -
496B PHE* 4.0 3.5 - - - -
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Residues in contact with THR 441 (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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373B ILE* 3.6 3.1 - - - -
374B ILE* 2.9 52.3 + - + +
375B SER 4.0 0.7 - - - +
379B ALA* 3.8 11.7 - - + -
440B PHE* 1.3 77.2 - - - +
442B ILE* 1.3 66.1 + - - +
443B LEU 3.7 0.7 + - - -
462B LEU* 3.6 11.3 - - + +
463B SER 2.8 30.1 + - - -
464B LEU 4.5 3.6 - - - -
466B VAL* 4.8 2.5 - - - +
496B PHE* 3.4 31.2 - - + -
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B PRO* 3.7 22.4 - - + -
342B LEU* 5.0 6.3 - - + -
348B PHE* 3.6 34.5 - - + -
371B ALA* 4.2 12.6 - - + -
372B THR 3.7 5.8 - - - +
373B ILE* 4.4 9.2 - - + +
396B ILE* 4.4 13.5 - - + -
419B MET* 4.6 4.7 - - + -
441B THR* 1.3 75.6 + - - +
443B LEU* 1.3 60.3 + - - +
444B PHE* 3.4 33.6 - - + -
462B LEU* 3.8 0.2 - - - -
463B SER* 2.7 43.9 + - - +
466B VAL* 5.5 6.5 - - + +
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Residues in contact with LEU 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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370B LYS 3.7 1.7 - - - +
371B ALA* 3.3 3.3 - - - -
372B THR* 2.8 47.8 + - + +
374B ILE* 4.0 21.3 - - + -
382B LEU* 4.4 11.4 - - + -
441B THR 3.7 1.2 + - - -
442B ILE* 1.3 72.5 - - - +
444B PHE* 1.3 70.7 + - - +
445B GLU* 3.9 25.1 - - + +
460B LYS* 4.0 25.4 - - + -
461B THR 3.3 18.8 - - - +
462B LEU* 3.7 21.8 - - + -
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Residues in contact with PHE 444 (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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332B PHE* 3.8 10.3 - - + -
334B ILE* 3.9 17.0 - - + -
338B PRO* 4.8 1.6 - - + -
350B ALA* 4.0 21.5 - - + -
352B VAL* 3.6 27.4 - - + -
369B VAL* 4.5 4.0 - - + -
370B LYS 3.5 2.7 - - - +
371B ALA* 3.5 27.4 - - + -
416B PHE* 3.7 27.4 - + - -
419B MET* 4.3 3.4 - - + -
442B ILE* 3.4 30.1 - - + -
443B LEU* 1.3 73.7 - - - +
445B GLU* 1.3 61.3 + - - +
460B LYS* 3.3 2.6 - - - -
461B THR* 2.9 54.7 + - + +
463B SER* 4.4 6.3 - - - -
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Residues in contact with GLU 445 (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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332B PHE* 4.5 1.3 - - - -
368B GLN 4.2 0.3 - - - +
369B VAL* 3.5 3.8 - - - +
370B LYS* 2.9 47.7 + - + +
372B THR* 4.4 10.4 - - - +
443B LEU* 3.9 27.6 - - + +
444B PHE* 1.3 76.9 - - - +
446B SER* 1.3 63.0 + - - +
459B VAL 3.5 9.6 - - - +
460B LYS* 4.4 10.9 - - + +
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Residues in contact with SER 446 (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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332B PHE* 4.2 13.9 - - - -
367B PRO* 3.3 22.4 - - - +
368B GLN 3.0 21.7 + - - -
369B VAL* 4.1 10.8 - - - -
403B MET* 4.1 5.6 - - - +
445B GLU* 1.3 77.7 - - - +
447B GLN* 1.3 70.4 + - - +
448B PHE* 4.8 0.7 - - - -
458B GLN* 3.7 1.7 - - - +
459B VAL* 2.9 36.7 + - - +
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Residues in contact with GLN 447 (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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367B PRO* 3.2 16.6 - - - +
368B GLN 4.5 2.3 + - - +
446B SER* 1.3 79.7 + - - +
448B PHE* 1.3 65.7 + - - +
456B VAL* 5.2 10.4 - - + +
457B PHE 3.1 13.7 - - - +
458B GLN* 3.4 31.6 + - + +
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Residues in contact with PHE 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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328B VAL* 4.7 14.4 - - + -
354B LEU* 3.6 35.4 - - + -
361B ASN 5.9 0.9 - - - +
365B ASN* 4.5 10.3 - - + +
367B PRO* 3.5 31.0 - - + -
403B MET* 4.7 2.9 - - + -
446B SER* 4.3 1.3 - - - -
447B GLN* 1.3 79.8 - - - +
449B SER* 1.3 68.4 + - - +
450B VAL* 4.6 7.2 - - + -
456B VAL* 3.5 4.3 - - - +
457B PHE* 2.9 58.9 + + + +
459B VAL* 3.7 31.9 - - + -
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Residues in contact with SER 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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361B ASN* 3.7 20.1 - - - +
365B ASN* 5.2 11.5 - - - +
448B PHE* 1.3 81.6 - - - +
450B VAL* 1.3 65.8 + - - +
451B GLY 4.0 1.1 - - - -
452B GLY 4.3 4.3 - - - -
453B ASN* 3.1 28.7 + - - -
455B LEU 3.3 10.1 + - - -
456B VAL* 4.3 5.7 - - - +
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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