Contacts of the strand formed by residues 565 - 574 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A THR* 3.2 29.0 - - + +
539A ILE* 4.4 13.1 + - + +
564A THR* 1.3 77.5 - - - +
566A TYR* 1.3 64.5 + - - +
567A MET* 5.0 12.1 - - + -
585A THR* 3.4 25.8 - - + -
586A PHE 3.2 22.7 - - - +
587A THR* 4.3 9.9 - - + -
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Residues in contact with TYR 566 (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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536A TYR* 5.0 14.1 - + + -
537A ARG* 3.6 10.5 - - - +
538A THR* 3.4 25.4 - - - -
557A LEU* 6.0 0.9 - - + -
559A SER 4.6 1.6 + - - -
560A LEU* 3.5 38.3 - - + +
561A THR* 2.9 41.7 + - - -
564A THR* 4.5 16.4 - - + -
565A LEU* 1.3 77.7 - - - +
567A MET* 1.3 62.5 + - - +
568A VAL* 4.2 4.3 - - + -
585A THR* 3.2 21.7 - - - +
586A PHE* 3.1 52.7 + + + -
588A THR* 5.2 4.9 - - - -
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Residues in contact with MET 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A PHE 4.3 0.3 - - - -
536A TYR* 3.1 23.9 - - - -
537A ARG* 2.9 30.3 + - + +
538A THR 4.5 3.4 - - - +
539A ILE* 4.4 27.6 - - - -
565A LEU* 5.0 8.7 - - + +
566A TYR* 1.3 76.5 - - - +
568A VAL* 1.3 61.8 + - - +
584A PHE 3.4 5.2 - - - +
585A THR* 4.3 15.7 - - + +
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Residues in contact with VAL 568 (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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503A VAL* 4.6 8.3 - - + -
515A LEU* 3.7 22.7 - - + -
534A ILE* 3.7 22.9 - - + -
535A PHE 3.3 11.7 - - - +
536A TYR* 3.7 13.5 - - + -
557A LEU* 4.6 3.8 - - + -
566A TYR* 4.8 0.7 - - + -
567A MET* 1.3 80.0 - - - +
569A ARG* 1.3 66.2 + - - +
583A GLU* 3.6 1.5 - - - +
584A PHE* 2.7 57.4 + - + +
586A PHE* 4.0 26.5 - - + -
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Residues in contact with ARG 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A VAL* 5.0 2.7 - - - -
534A ILE* 3.8 1.4 - - - -
535A PHE* 2.9 63.5 + - + +
543A GLU* 3.2 31.9 + - - -
568A VAL* 1.3 78.8 - - - +
570A MET* 1.3 71.0 + - - +
580A ASP* 3.4 32.2 + - + -
581A GLY 4.6 6.1 - - - +
582A PRO 4.4 7.4 - - - +
583A GLU* 4.2 17.9 - - + +
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Residues in contact with MET 570 (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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501A PRO* 4.1 22.4 + - + +
503A VAL* 3.9 24.0 - - + +
515A LEU* 6.0 1.1 - - - -
517A TRP* 3.4 63.5 - - + +
532A TYR* 3.6 31.6 - - + -
533A THR 3.3 3.8 - - - +
534A ILE* 4.0 25.1 - - + -
535A PHE* 4.9 0.2 - - - -
568A VAL* 5.2 0.2 - - + -
569A ARG* 1.3 80.7 - - - +
571A ALA* 1.3 61.8 + - - +
580A ASP* 3.3 4.7 - - - +
581A GLY* 2.8 28.1 + - - +
582A PRO 5.2 0.6 + - - -
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Residues in contact with ALA 571 (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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501A PRO* 3.9 4.3 - - - -
532A TYR* 3.1 11.4 - - - +
533A THR 2.9 31.8 + - - +
535A PHE* 4.0 4.3 - - + -
570A MET* 1.3 75.7 - - - +
572A ALA* 1.3 60.8 + - - +
573A TYR* 3.5 32.5 - - + +
579A LYS 3.2 9.9 - - - +
580A ASP* 3.6 19.3 - - - +
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Residues in contact with ALA 572 (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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497A PRO* 3.6 22.0 - - + +
499A LYS 4.7 0.9 - - - +
501A PRO* 3.8 21.1 - - + +
520A LEU* 4.1 15.9 - - + -
529A ILE* 4.2 7.6 - - + -
531A ASN 4.0 3.6 - - - -
532A TYR* 4.4 4.9 - - + -
571A ALA* 1.3 75.5 - - - +
573A TYR* 1.3 61.6 + - - +
578A GLY* 2.9 3.5 - - - -
579A LYS 2.9 30.6 + - - +
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Residues in contact with TYR 573 (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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529A ILE* 3.4 6.3 - - - +
530A ARG* 2.8 28.1 + - + -
531A ASN* 3.1 41.4 + - - +
533A THR* 3.1 34.6 - - - +
535A PHE* 3.9 12.5 - - - -
571A ALA* 3.5 26.6 - - + +
572A ALA* 1.3 74.4 - - - +
574A THR* 1.3 68.3 - - - +
577A GLY* 3.4 5.6 - - - +
578A GLY* 3.4 26.2 - - - -
580A ASP* 5.1 0.9 + - - -
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Residues in contact with THR 574 (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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494A GLN* 4.7 2.0 - - - -
495A ALA 3.0 29.1 + - - +
496A PRO 3.5 0.2 - - - -
497A PRO* 3.5 13.0 - - + -
525A GLN 3.5 25.1 - - - +
527A GLY* 3.7 22.9 - - - +
528A PHE 3.7 8.3 - - - -
529A ILE* 3.8 4.9 - - + -
530A ARG* 4.4 5.5 - - - +
573A TYR* 1.3 79.2 - - - +
575A ASP* 1.3 61.5 + - - +
576A GLU 2.9 12.5 + - - -
577A GLY* 2.7 24.2 + - - +
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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