Contacts of the strand formed by residues 547 - 558 (chain A) in PDB entry 2E3M
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 ILE 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A LYS* 3.6 3.8 - - - +
426A GLY* 2.6 48.7 + - - +
427A VAL* 3.6 19.7 - - - +
428A THR* 3.6 28.5 - - + -
531A THR* 4.5 2.2 - - + -
532A LEU 3.4 5.6 - - - +
533A VAL* 3.6 27.8 - - + -
542A ILE* 4.2 3.8 - - + -
543A SER 3.8 11.4 - - - +
544A ARG* 3.7 7.4 - - - +
545A ASP 3.3 4.0 + - - +
546A ASN* 1.3 85.2 - - - +
548A LEU* 1.3 57.9 + - - +
596A ILE* 3.9 19.5 - - + -
598A PHE* 4.1 8.1 - - + -
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Residues in contact with LEU 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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423A ALA* 3.9 8.3 - - + -
424A VAL 3.6 25.6 - - - +
425A LYS* 3.6 39.9 - - + +
427A VAL 4.0 2.7 - - - -
531A THR* 3.6 1.9 - - - -
532A LEU* 2.9 50.8 + - + +
547A ILE* 1.3 76.0 - - - +
549A CYS* 1.3 64.9 + - - +
550A LYS* 3.8 25.4 + - + -
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Residues in contact with CYS 549 (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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423A ALA* 3.5 3.8 - - - -
424A VAL* 2.9 38.7 + - + +
427A VAL* 3.5 32.0 + - + +
428A THR 4.2 0.7 - - - -
429A GLY* 3.6 16.6 - - - -
432A VAL* 3.9 14.6 - - + -
529A CYS* 3.6 31.0 - - - -
530A GLN 3.5 4.7 - - - -
531A THR* 4.5 2.0 - - - +
548A LEU* 1.3 71.9 - - - +
550A LYS* 1.3 61.0 + - - +
551A ILE* 3.7 11.1 + - - +
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Residues in contact with LYS 550 (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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421A THR* 6.4 0.6 - - - -
422A HIS 3.7 6.1 + - - +
423A ALA* 4.5 13.5 - - + +
528A ILE 3.5 1.4 - - - +
529A CYS* 3.3 5.4 - - - -
530A GLN* 2.7 41.6 + - + +
532A LEU* 3.8 35.4 - - + -
548A LEU* 3.9 22.9 - - + +
549A CYS* 1.3 70.5 - - - +
551A ILE* 1.3 61.0 + - - +
552A THR 4.1 0.2 + - - -
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Residues in contact with ILE 551 (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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420A ALA 5.3 0.7 - - - +
421A THR* 3.3 6.6 - - - +
422A HIS* 2.8 45.2 + - + +
424A VAL* 3.8 16.6 - - + -
432A VAL* 4.0 18.2 - - + -
527A MET* 3.9 23.8 - - - -
528A ILE 3.4 4.7 - - - +
529A CYS* 4.0 6.3 - - - -
549A CYS* 3.9 20.4 - - - +
550A LYS* 1.3 76.7 - - - +
552A THR* 1.3 73.7 + - - +
553A TYR* 4.2 5.8 - - + +
580A LEU* 5.0 4.5 - - + -
584A THR* 3.6 31.9 - - + -
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Residues in contact with THR 552 (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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382A SER 3.4 14.8 - - - +
383A LEU* 4.1 21.1 + - + +
419A LYS* 3.4 29.7 + - + +
420A ALA 3.4 7.4 - - - +
421A THR* 3.9 10.2 - - - +
527A MET* 3.7 0.5 - - - -
528A ILE* 2.6 51.4 + - + +
550A LYS 4.1 0.2 + - - -
551A ILE* 1.3 76.5 + - - +
553A TYR* 1.3 60.5 + - - +
554A VAL* 4.2 9.6 - - + -
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Residues in contact with TYR 553 (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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418A LEU* 4.0 9.6 - - + -
419A LYS* 3.4 2.3 - - - +
420A ALA* 2.8 42.2 + - + +
436A PHE* 4.4 4.9 - + - -
525A VAL* 3.8 27.6 - - + +
526A ALA 3.3 13.2 - - - -
527A MET* 4.0 16.6 - - + -
551A ILE* 4.2 7.4 - - + -
552A THR* 1.3 75.1 - - - +
554A VAL* 1.3 66.6 + - - +
555A ALA* 3.7 17.4 - - + +
576A TYR* 3.4 37.0 - + - -
579A PHE* 3.5 31.0 - + - -
580A LEU* 4.0 27.8 - - + -
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Residues in contact with VAL 554 (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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378A HIS* 3.5 33.4 - - + +
382A SER* 3.6 27.1 - - - +
392A TRP* 6.0 1.6 - - + -
418A LEU 3.4 3.8 - - - +
419A LYS* 3.8 28.0 - - + -
524A ASN 4.6 0.7 - - - -
525A VAL* 3.3 7.4 - - - +
526A ALA* 2.8 47.1 + - + +
528A ILE* 4.7 2.9 - - + -
552A THR* 4.3 3.1 - - + -
553A TYR* 1.3 80.8 - - - +
555A ALA* 1.3 62.4 + - - +
556A ASN* 4.7 7.6 - - - +
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Residues in contact with ALA 555 (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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416A ASP 4.2 2.1 - - - +
417A PRO* 3.7 1.2 - - - +
418A LEU* 2.9 43.5 + - + +
524A ASN 3.8 3.6 - - - -
525A VAL* 3.9 9.2 - - + -
553A TYR* 3.7 12.3 - - + +
554A VAL* 1.3 75.5 - - - +
556A ASN* 1.3 64.2 + - - +
557A VAL* 4.0 1.7 + - + -
576A TYR* 3.7 38.8 - - + +
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Residues in contact with ASN 556 (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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378A HIS* 4.8 4.8 - - - -
415A LEU 5.0 2.9 - - - +
417A PRO* 3.4 32.8 - - - +
418A LEU 5.5 0.2 + - - -
522A LYS 3.8 1.4 - - - +
523A ILE* 3.4 1.7 - - - -
524A ASN* 2.7 65.4 + - + +
554A VAL* 4.7 9.7 - - - +
555A ALA* 1.3 80.0 - - - +
557A VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 557 (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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414A VAL 4.2 0.3 - - - +
415A LEU* 4.0 23.4 + - - +
416A ASP 5.4 1.4 + - - -
521A ALA* 4.6 5.8 - - + -
522A LYS 3.5 2.5 - - - -
523A ILE* 3.8 28.5 - - + -
525A VAL* 4.5 5.6 - - + -
555A ALA* 4.0 5.7 - - + -
556A ASN* 1.3 82.3 - - - +
558A ASN* 1.3 71.4 + - - +
559A PRO* 3.4 17.3 - - + +
576A TYR* 3.6 24.0 - - - +
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Residues in contact with ASN 558 (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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413A ILE* 4.1 15.6 - - - +
415A LEU* 3.7 27.1 - - + +
521A ALA* 3.1 3.1 - - - +
522A LYS* 2.7 55.3 + - + +
557A VAL* 1.3 73.9 - - - +
559A PRO* 1.4 66.3 - - - +
560A GLY* 2.7 33.7 + - - -
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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