Contacts of the strand formed by residues 533 - 543 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A GLY 3.6 2.4 + - - -
450A THR* 3.8 11.4 - - - +
452A GLY 3.3 14.6 - - - -
454A SER* 3.7 10.4 - - - -
529A GLN* 3.6 1.6 - - - +
530A THR* 2.9 35.0 + - - +
531A PRO 3.6 0.2 - - - -
532A PHE* 1.3 82.2 - - - +
534A VAL* 1.3 64.0 + - - -
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Residues in contact with VAL 534 (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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450A THR 4.9 1.1 - - - +
452A GLY 3.0 21.1 + - - +
453A PRO* 3.9 1.9 - - + +
454A SER* 3.1 17.8 + - - +
457A GLY* 3.4 12.0 - - - +
527A PRO* 4.8 7.4 - - + -
528A VAL 3.7 9.0 - - - +
529A GLN* 3.3 29.4 - - + +
533A GLY* 1.3 74.5 - - - -
535A VAL* 1.3 74.6 + - - +
536A THR* 4.6 12.6 - - + +
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Residues in contact with VAL 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLY 5.9 0.7 - - - +
377A ILE* 4.6 8.7 - - + -
436A SER* 3.6 17.5 - - - +
454A SER* 3.6 20.0 - - - +
457A GLY 3.4 2.7 - - - -
458A PHE* 4.2 2.7 - - - -
459A GLU* 4.0 24.9 - - + -
527A PRO* 3.2 2.9 - - - +
528A VAL* 3.0 37.3 + - + +
530A THR* 3.9 16.2 - - + +
534A VAL* 1.3 82.2 - - - +
536A THR* 1.3 74.0 + - - +
537A PHE* 4.0 14.7 - - + -
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Residues in contact with THR 536 (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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457A GLY 3.0 15.9 + - - +
458A PHE* 3.1 28.6 - - - +
459A GLU 3.1 4.7 + - - -
521A GLU* 6.5 1.3 - - - -
527A PRO* 3.9 25.6 - - + -
534A VAL* 4.6 9.0 - - + -
535A VAL* 1.3 79.3 - - - +
537A PHE* 1.3 67.0 + - - +
538A LEU* 5.3 3.8 - - - +
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Residues in contact with PHE 537 (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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377A ILE* 4.1 30.3 - - + -
380A GLU* 4.7 1.8 - - + -
431A ILE* 4.3 2.2 - - + -
459A GLU* 3.5 28.3 - - + -
461A THR* 4.1 14.8 - - + -
521A GLU* 3.7 5.7 - - - +
522A ASP* 3.0 24.8 + - + -
525A MET* 3.3 57.7 + - + +
526A GLN 3.6 25.1 - - - -
527A PRO* 5.5 1.4 - - - +
528A VAL* 4.0 11.9 - - + -
535A VAL* 4.0 18.6 - - + -
536A THR* 1.3 82.2 - - - +
538A LEU* 1.3 61.8 + - - +
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Residues in contact with LEU 538 (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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458A PHE* 4.0 29.1 - - + +
459A GLU 3.1 8.5 + - - +
460A LEU* 3.3 11.9 - - + +
461A THR* 2.7 30.7 + - - -
495A PHE* 3.7 40.2 - - + +
496A CYS* 4.0 1.8 - - - +
497A SER* 3.8 32.1 - - - +
519A LEU* 4.1 14.8 - - + -
520A THR 3.7 15.5 - - - +
521A GLU* 4.4 3.8 - - + +
536A THR* 4.2 4.6 - - - +
537A PHE* 1.3 73.5 - - - +
539A GLN* 1.3 53.5 + - - +
540A ILE 4.1 0.3 + - - -
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Residues in contact with GLN 539 (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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461A THR* 3.1 21.8 - - - +
462A PHE* 4.4 2.0 - - - -
463A ARG* 2.9 37.1 + - - +
518A LEU 3.7 0.3 - - - +
519A LEU* 3.5 6.4 - - - -
520A THR* 2.7 44.0 + - + +
522A ASP* 3.8 8.7 - - - +
523A PRO* 3.1 16.2 - - - +
537A PHE 3.9 0.4 + - - -
538A LEU* 1.3 72.9 - - - +
540A ILE* 1.3 74.3 + - - +
541A VAL* 4.2 1.9 - - + +
573A TRP 3.0 11.9 + - - -
574A LEU* 2.7 36.1 + - - +
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Residues in contact with ILE 540 (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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460A LEU* 4.5 9.2 - - + -
461A THR 2.8 14.9 + - - +
462A PHE* 3.5 36.9 - - + -
463A ARG 4.6 0.7 + - - -
480A LEU* 4.7 9.9 - - + -
481A MET* 4.1 28.5 - - + -
484A LEU* 3.6 30.7 - - + -
507A LEU* 5.2 0.4 - - + -
517A MET* 3.4 37.0 - - + -
518A LEU 3.7 3.6 - - - -
519A LEU* 3.9 8.5 - - + -
539A GLN* 1.3 88.4 + - - +
541A VAL* 1.3 64.5 + - - +
576A THR* 4.2 1.6 + - - -
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Residues in contact with VAL 541 (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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517A MET* 3.4 3.9 - - - -
518A LEU* 2.9 37.1 + - + +
520A THR* 3.7 29.8 - - + -
539A GLN* 4.0 4.3 - - - +
540A ILE* 1.3 81.5 - - - +
542A GLY* 1.3 70.8 + - - +
543A VAL* 3.5 2.4 + - - +
560A LEU* 4.3 7.9 - - + -
563A LEU* 4.1 22.7 - - + -
569A ALA 5.0 5.6 - - - +
574A LEU* 4.0 33.7 - - + +
575A ILE 5.7 0.2 - - - -
576A THR* 3.7 5.2 - - - +
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Residues in contact with GLY 542 (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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462A PHE* 4.5 3.0 - - - -
507A LEU* 3.9 7.0 - - - -
514A ILE* 3.3 24.1 - - - +
516A HIS 3.3 9.2 - - - -
540A ILE* 4.2 1.0 - - - +
541A VAL* 1.3 78.0 - - - +
543A VAL* 1.3 65.3 + - - +
563A LEU* 5.1 0.2 - - - +
569A ALA 5.0 1.4 - - - +
576A THR* 2.9 25.2 + - - +
580A ARG* 4.3 12.3 + - - -
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Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE* 3.4 9.7 - - - +
515A GLN 3.0 21.8 + - - -
516A HIS* 3.1 38.3 + - + -
517A MET* 3.7 5.4 - - - +
518A LEU* 3.9 20.6 - - + -
541A VAL 3.6 7.9 - - - +
542A GLY* 1.3 79.6 - - - +
544A CYS* 1.3 65.2 + - - +
547A GLU* 3.4 16.8 - - + +
548A LEU* 4.3 10.8 - - + +
563A LEU* 3.7 27.8 - - + -
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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