Contacts of the strand formed by residues 541 - 548 (chain A) in PDB entry 3FO5
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 LEU 541 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A VAL* 3.6 22.4 - - + -
432A VAL 3.5 11.0 - - - +
433A HIS* 4.5 9.0 - - + +
436A ALA* 4.9 1.6 + - - +
536A ARG* 3.8 2.4 - - - -
537A GLU* 2.9 53.8 + - + +
538A GLY* 3.5 10.0 + - - +
539A ASP 3.1 7.3 - - - +
540A GLN* 1.3 80.8 - - - +
542A THR* 1.3 63.8 + - - +
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Residues in contact with THR 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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431A VAL* 3.3 5.9 - - - +
432A VAL 2.9 34.1 + - - -
434A VAL* 2.6 30.8 + - - -
435A ASP 3.3 0.3 - - - -
436A ALA* 2.8 29.1 + - + -
439A ALA* 4.4 3.4 - - + -
534A LEU* 3.8 22.2 - - + -
535A TRP 3.3 11.0 - - - +
541A LEU* 1.3 72.2 + - - +
543A LYS* 1.3 74.3 + - - +
544A VAL* 3.4 13.3 + - + +
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Residues in contact with LYS 543 (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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429A GLU* 3.7 36.2 + - + -
430A MET 3.5 10.5 - - - +
431A VAL* 4.2 13.5 - - + -
533A CYS 3.5 2.6 - - - +
534A LEU* 3.3 7.8 - - - -
535A TRP* 2.8 57.8 + - + +
537A GLU* 3.4 34.4 + - + +
542A THR* 1.3 71.0 - - - +
544A VAL* 1.3 59.3 + - - +
545A SER* 4.4 1.8 - - - +
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Residues in contact with VAL 544 (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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429A GLU* 3.5 2.1 - - - -
430A MET* 2.8 47.5 + - + +
432A VAL* 3.9 19.3 - - + -
439A ALA* 5.1 1.1 - - + -
443A LEU* 4.0 14.4 - - + -
532A PHE* 4.3 7.9 - - + -
534A LEU* 3.9 17.9 - - + -
542A THR* 3.8 24.0 - - + +
543A LYS* 1.3 73.0 - - - +
545A SER* 1.3 62.3 + - - +
573A PHE* 3.6 19.7 - - + -
576A CYS* 4.9 1.3 - - - -
580A LEU* 4.1 15.0 - - + -
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Residues in contact with SER 545 (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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427A HIS* 4.3 2.6 - - - -
428A MET 3.1 10.1 - - - -
429A GLU* 3.7 22.5 + - - +
531A GLY 3.8 0.2 - - - +
532A PHE* 3.1 10.4 - - - +
533A CYS 2.9 39.3 + - - -
535A TRP* 3.7 16.9 - - - -
543A LYS* 4.4 1.4 - - - +
544A VAL* 1.3 75.3 + - - +
546A TYR* 1.3 59.5 + - - +
547A TYR* 3.6 24.5 + - - -
573A PHE* 4.3 0.7 - - - -
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Residues in contact with TYR 546 (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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2A 1PE 2.6 59.4 + - - -
426A PHE* 3.9 18.8 - + - -
427A HIS* 3.0 5.5 - - - +
428A MET* 2.8 35.4 + - + -
449A ARG* 3.9 13.5 - - - -
530A SER* 3.9 0.9 - - - -
531A GLY* 3.3 20.4 - - - -
532A PHE* 3.9 24.2 - + + -
545A SER* 1.3 74.1 - - - +
547A TYR* 1.3 78.3 + - - +
548A ASN* 3.0 32.1 + - + -
573A PHE* 3.7 23.8 - - + -
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Residues in contact with TYR 547 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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395A LEU* 3.8 25.6 - - + -
398A LEU* 3.9 13.9 - - + -
399A VAL* 3.5 45.6 + - + +
404A TRP* 3.7 22.2 - + - -
426A PHE 3.6 2.7 - - - -
427A HIS* 3.4 43.3 + + + -
429A GLU* 5.3 0.5 + - - -
530A SER* 3.0 6.3 - - - -
531A GLY 2.8 36.7 + - - +
533A CYS* 4.3 8.7 - - + -
535A TRP* 4.3 5.5 - - - -
545A SER* 3.6 25.7 + - - -
546A TYR* 1.3 83.4 - - - +
548A ASN* 1.3 60.3 + - - +
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Residues in contact with ASN 548 (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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2A 1PE 4.2 13.7 - - - -
398A LEU* 4.8 1.1 - - - -
425A SER* 3.2 1.3 - - - -
426A PHE* 2.9 65.3 + - + -
527A THR* 3.9 1.4 + - - -
530A SER* 3.2 13.4 + - - -
546A TYR* 3.0 22.9 + - + +
547A TYR* 1.3 74.6 - - - +
549A GLN* 1.3 61.2 + - - +
550A ALA 3.6 4.2 + - - -
551A THR* 2.6 31.5 + - - -
595A GOL 3.1 16.4 + - - -
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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