Contacts of the strand formed by residues 533 - 543 (chain B) in PDB entry 4BL8
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 GLY 533 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449B GLY 3.6 2.8 + - - -
450B THR* 3.7 13.0 - - - +
452B GLY 3.4 12.8 - - - -
454B SER* 3.8 8.7 - - - -
529B GLN* 3.4 2.4 - - - +
530B THR* 2.9 35.1 + - - +
531B PRO 3.7 0.2 - - - -
532B PHE* 1.3 81.1 - - - +
534B VAL* 1.3 63.4 + - - -
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Residues in contact with VAL 534 (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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450B THR 4.8 2.0 - - - +
452B GLY 3.0 21.5 + - - +
453B PRO* 3.9 2.3 - - + +
454B SER* 3.1 20.0 + - - +
457B GLY* 3.6 10.1 - - - +
527B PRO* 4.8 7.6 - - + -
528B VAL 3.7 8.5 - - - +
529B GLN* 3.3 29.6 - - + +
533B GLY* 1.3 74.6 - - - -
535B VAL* 1.3 70.4 + - - +
536B THR* 4.2 13.5 - - + +
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Residues in contact with VAL 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B GLY* 5.7 1.1 - - - +
376B ALA* 6.2 0.7 - - + -
377B ILE* 4.7 8.5 - - + -
436B SER* 3.7 17.0 - - - +
454B SER* 3.5 20.9 - - - +
457B GLY 3.6 2.7 - - - -
458B PHE* 4.4 2.2 - - - -
459B GLU* 4.0 23.8 - - + -
527B PRO* 3.2 3.2 - - - +
528B VAL* 3.0 36.9 + - + +
530B THR* 3.9 17.5 - - + +
534B VAL* 1.3 83.5 - - - +
536B THR* 1.3 72.3 + - - +
537B PHE* 3.9 15.5 - - + -
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Residues in contact with THR 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B GLY 3.0 14.7 + - - +
458B PHE* 3.1 28.7 - - - +
459B GLU 3.2 4.2 + - - -
521B GLU* 6.5 1.1 - - - -
527B PRO* 3.9 27.1 - - + -
534B VAL* 4.6 9.6 - - + -
535B VAL* 1.3 79.1 - - - +
537B PHE* 1.3 66.6 + - - +
538B LEU* 5.2 3.8 - - - +
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Residues in contact with PHE 537 (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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377B ILE* 4.2 21.3 - - + -
380B GLU* 4.4 5.4 - - + -
431B ILE* 4.4 4.0 - - + -
459B GLU* 3.6 33.2 - - + +
461B THR* 4.1 11.9 - - + -
521B GLU* 3.7 5.5 - - - +
522B ASP* 3.0 23.9 + - + +
525B MET* 3.3 60.4 + - + +
526B GLN 3.6 25.6 - - - -
527B PRO* 5.5 1.4 - - - +
528B VAL* 4.0 12.6 - - + -
535B VAL* 3.9 20.2 - - + -
536B THR* 1.3 78.9 - - - +
538B LEU* 1.3 61.8 + - - +
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Residues in contact with LEU 538 (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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458B PHE* 3.9 31.8 - - + +
459B GLU 3.1 8.1 + - - +
460B LEU* 3.3 9.2 - - + +
461B THR* 2.8 25.8 + - - -
495B PHE* 3.1 41.3 - - + +
496B CYS* 4.2 1.3 - - - +
497B SER* 4.1 29.6 - - - +
519B LEU* 4.1 15.5 - - + -
520B THR 3.8 17.0 - - - +
521B GLU* 4.4 4.7 - - + +
536B THR* 4.2 4.6 + - - +
537B PHE* 1.3 75.0 - - - +
539B GLN* 1.3 60.3 + - - +
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Residues in contact with GLN 539 (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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461B THR* 3.1 22.4 - - - +
462B PHE* 4.5 2.5 - - - -
463B ARG* 3.0 44.5 + - - +
518B LEU 3.7 0.5 - - - +
519B LEU* 3.5 7.1 - - - -
520B THR* 2.7 42.6 + - + +
522B ASP* 3.8 8.7 - - - -
523B PRO* 3.0 18.1 - - - +
537B PHE 3.9 0.6 + - - -
538B LEU* 1.3 72.7 - - - +
540B ILE* 1.3 77.6 + - - +
541B VAL* 3.9 15.5 - - + +
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Residues in contact with ILE 540 (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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460B LEU* 4.4 11.0 - - + -
461B THR 2.8 14.7 + - - +
462B PHE* 3.5 35.3 - - + -
463B ARG 4.7 0.5 + - - -
480B LEU* 4.7 10.1 - - + -
481B MET* 4.1 27.6 - - + -
484B LEU* 3.5 31.2 - - + -
507B LEU* 5.2 0.4 - - + -
517B MET* 3.4 37.7 - - + -
518B LEU 3.8 3.4 - - - -
519B LEU* 4.0 9.0 - - + -
539B GLN* 1.3 87.2 + - - +
541B VAL* 1.3 63.9 + - - +
542B GLY 4.6 0.2 - - - +
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Residues in contact with VAL 541 (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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462B PHE* 5.0 0.4 - - - -
517B MET* 3.4 3.1 - - - -
518B LEU* 2.9 41.9 + - + +
520B THR* 3.7 30.1 - - + -
539B GLN* 3.9 13.5 - - - +
540B ILE* 1.3 81.8 - - - +
542B GLY* 1.3 73.4 + - - +
543B VAL* 3.5 8.6 + - + +
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Residues in contact with GLY 542 (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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462B PHE* 4.5 10.2 - - - -
507B LEU* 3.8 9.0 - - - -
514B ILE* 3.3 27.5 - - - +
516B HIS 3.3 9.2 - - - -
540B ILE* 4.2 1.4 + - - +
541B VAL* 1.3 78.7 - - - +
543B VAL* 1.3 64.2 + - - +
547B GLU* 4.9 0.2 - - - +
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Residues in contact with VAL 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B ILE* 3.3 9.5 - - - +
515B GLN 3.0 21.8 + - - -
516B HIS* 3.1 38.0 + - + -
517B MET* 3.7 6.1 - - - +
518B LEU* 3.9 29.2 - - + -
541B VAL* 3.5 13.5 - - + +
542B GLY* 1.3 81.9 - - - +
544B CYS* 1.3 65.5 + - - +
547B GLU* 3.4 19.3 - - + +
548B LEU* 4.3 10.1 - - + +
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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