Contacts of the strand formed by residues 565 - 573 (chain B) in PDB entry 3L5J
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 565 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538B THR* 3.0 26.0 + - - -
539B ILE* 4.0 21.2 - - + +
564B THR* 1.3 74.8 - - - +
566B TYR* 1.3 67.8 + - - +
567B MET* 4.7 17.6 - - + +
585B THR* 3.1 27.8 - - - +
586B PHE* 3.4 14.1 - - - +
587B THR* 3.6 22.6 - - + +
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Residues in contact with TYR 566 (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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536B TYR* 4.5 22.4 - + + -
537B ARG* 3.4 18.8 - - - -
538B THR* 3.4 28.1 - - + +
557B LEU* 6.2 1.6 - - + -
559B SER 4.9 0.7 + - - -
560B LEU* 3.9 18.5 - - + -
561B THR* 3.4 45.9 + - - -
564B THR* 4.1 11.2 - - - -
565B LEU* 1.3 79.2 - - - +
567B MET* 1.3 64.1 + - - +
568B VAL* 4.1 6.3 + - + +
585B THR* 3.3 7.1 + - - -
586B PHE* 3.0 60.7 + + + -
588B THR* 5.0 2.7 - - + -
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Residues in contact with MET 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B PHE 3.7 0.2 - - - +
536B TYR* 3.1 25.3 - - - +
537B ARG* 3.1 39.4 + - + +
538B THR* 4.2 16.2 - - - -
539B ILE* 4.7 6.3 - - + +
565B LEU* 4.7 18.6 - - + +
566B TYR* 1.3 77.5 - - - +
568B VAL* 1.3 62.9 + - - +
583B GLU* 6.4 1.8 - - + -
584B PHE 3.4 8.7 - - - +
585B THR* 4.9 7.9 - - - +
590B CL 3.9 14.1 - - + +
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Residues in contact with VAL 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B VAL* 4.8 6.7 - - + -
515B LEU* 4.2 15.3 - - + -
534B ILE* 3.7 22.2 - - + -
535B PHE 3.2 11.7 - - - +
536B TYR* 4.3 9.6 - - + -
557B LEU* 4.8 3.1 - - + -
566B TYR* 4.3 4.9 - - + +
567B MET* 1.3 81.1 - - - +
569B ARG* 1.3 74.1 + - - +
570B MET* 5.6 1.1 - - + -
583B GLU* 3.5 2.9 - - - +
584B PHE* 2.8 49.3 + - + +
586B PHE* 3.8 31.9 - - + -
590B CL 4.5 1.8 - - - -
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Residues in contact with ARG 569 (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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503B VAL* 5.1 3.1 - - - -
534B ILE* 3.8 0.5 - - - -
535B PHE* 2.9 83.8 + - + +
537B ARG* 3.9 8.6 - - - +
543B GLU* 3.3 19.4 + - - -
568B VAL* 1.3 81.4 - - - +
570B MET* 1.3 62.6 + - - +
580B ASP* 2.8 35.9 + - - +
581B GLY 4.5 8.1 - - - +
582B PRO 4.5 5.2 - - - -
583B GLU* 4.1 28.0 - - + -
590B CL 3.6 16.0 - - + +
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Residues in contact with MET 570 (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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501B PRO* 3.8 25.2 + - + +
503B VAL* 4.5 18.4 - - + +
517B TRP* 3.5 54.1 - - + +
532B TYR* 3.4 45.5 - - + -
533B THR 3.4 3.4 - - - +
534B ILE* 3.6 27.8 - - + -
548B VAL* 5.2 0.4 - - + -
568B VAL* 5.6 0.9 - - + -
569B ARG* 1.3 75.3 - - - +
571B ALA* 1.3 55.7 + - - +
580B ASP* 4.4 1.3 - - - -
581B GLY* 2.7 34.4 + - - +
582B PRO 5.1 1.8 + - - -
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Residues in contact with ALA 571 (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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501B PRO* 4.3 2.5 - - - -
532B TYR* 3.3 8.6 - - - +
533B THR 3.0 29.5 + - - +
535B PHE* 4.1 8.0 - - + -
570B MET* 1.3 74.1 - - - +
572B ALA* 1.3 60.6 + - - +
573B TYR* 3.4 29.9 - - + +
578B GLY 5.3 0.2 - - - -
579B LYS 3.4 11.0 - - - +
580B ASP* 3.2 25.8 - - - +
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Residues in contact with ALA 572 (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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497B PRO* 3.4 15.1 - - + +
499B LYS 4.6 0.2 - - - +
501B PRO* 3.9 13.7 - - + +
520B LEU* 3.5 32.3 - - + -
529B ILE* 4.2 7.0 - - + -
531B ASN 4.0 4.0 - - - +
532B TYR* 4.3 8.5 - - + -
571B ALA* 1.3 73.9 - - - +
573B TYR* 1.3 60.8 + - - +
578B GLY* 3.0 2.3 - - - -
579B LYS 2.9 31.4 + - - +
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Residues in contact with TYR 573 (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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497B PRO* 4.7 0.2 - - - -
529B ILE* 3.5 8.0 - - - +
530B ARG* 2.9 26.8 + - + -
531B ASN* 3.0 35.2 + - - +
533B THR* 3.5 22.3 - - + +
535B PHE* 3.7 23.0 - - - -
571B ALA* 3.4 33.5 - - + +
572B ALA* 1.3 75.2 - - - +
574B THR* 1.3 67.2 + - - +
577B GLY* 3.5 4.5 - - - +
578B GLY* 3.3 28.7 - - - -
580B ASP* 4.8 1.2 + - - -
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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