Contacts of the strand formed by residues 522 - 533 (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 LYS 522 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506A SER* 3.4 28.0 + - - +
507A VAL* 5.4 2.3 + - - +
508A ASP* 4.5 15.4 + - - -
514A LEU* 6.5 0.4 - - - -
520A ARG* 3.9 17.9 + - + +
521A ALA* 1.3 80.0 - - - +
523A ILE* 1.3 60.4 + - - +
556A ASN 3.8 1.6 - - - +
557A VAL* 3.5 1.4 - - - -
558A ASN* 2.7 49.6 + - + +
560A GLY* 5.7 0.2 - - - -
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Residues in contact with ILE 523 (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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467A GLN* 6.1 0.4 - - - +
480A VAL* 3.8 21.8 - - + -
482A TYR* 3.9 28.7 - - + -
504A ASN* 4.0 20.9 - - + +
505A PHE* 3.3 2.4 - - - +
506A SER* 2.8 48.1 + - - +
521A ALA* 4.7 4.9 - - + -
522A LYS* 1.3 76.2 - - - +
524A ASN* 1.3 62.6 + - - +
525A VAL* 4.6 10.5 - - + -
556A ASN 3.4 4.3 - - - -
557A VAL* 3.8 29.2 - - + -
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Residues in contact with ASN 524 (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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374A MET* 3.1 30.8 - - + +
378A HIS* 2.8 33.7 + - - -
503A CYS* 6.1 0.3 - - - +
504A ASN 3.5 4.4 - - - +
505A PHE* 4.3 2.5 - - + +
523A ILE* 1.3 76.4 - - - +
525A VAL* 1.3 61.0 + - - +
554A VAL 4.6 0.2 - - - -
555A ALA* 3.8 0.3 - - - -
556A ASN* 2.7 52.9 + - + +
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Residues in contact with VAL 525 (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* 4.3 0.6 + - - -
436A PHE* 4.4 7.4 - - + -
502A VAL 3.8 0.2 - - - +
503A CYS* 3.5 3.1 - - - +
504A ASN* 2.7 59.8 + - + +
523A ILE* 4.6 11.7 - - + -
524A ASN* 1.3 81.7 + - - +
526A ALA* 1.3 65.6 + - - +
553A TYR* 3.8 26.5 - - + +
554A VAL 3.3 7.6 - - - +
555A ALA* 3.9 23.8 - - + -
557A VAL* 4.5 13.7 - - + -
576A TYR* 5.6 0.2 - - - +
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Residues in contact with ALA 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A HIS* 3.6 25.6 - - + +
501A ILE* 4.2 4.3 - - + -
502A VAL 3.2 9.2 - - - +
503A CYS* 4.7 0.4 - - - -
525A VAL* 1.3 79.5 - - - +
527A MET* 1.3 60.0 + - - +
528A ILE* 4.0 12.6 - - + -
552A THR 4.5 0.2 - - - -
553A TYR* 3.3 5.0 - - - -
554A VAL* 2.8 53.6 + - + +
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Residues in contact with MET 527 (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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432A VAL* 4.3 12.8 - - + -
433A CYS* 3.9 7.0 - - - -
436A PHE* 3.3 62.1 - - + -
500A TRP 3.9 0.7 - - - +
501A ILE* 3.3 5.0 - - - -
502A VAL* 3.1 28.4 + - + +
526A ALA* 1.3 71.5 - - - +
528A ILE* 1.3 59.3 + - - +
529A CYS* 4.2 11.2 - - - -
551A ILE* 3.9 26.2 - - - -
552A THR 3.7 2.5 - - - -
553A TYR* 4.0 11.2 - - + +
579A PHE* 3.8 14.8 - - + -
580A LEU* 4.8 3.6 - - + -
583A PHE* 3.7 17.5 - - + -
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Residues in contact with ILE 528 (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* 4.2 14.6 - - + +
379A MET* 4.4 7.0 - - - +
382A SER* 3.8 25.4 - - - -
383A LEU* 3.7 36.3 - - + -
499A THR* 3.4 30.1 - - + -
500A TRP 3.6 2.7 - - - +
501A ILE* 3.8 16.8 - - + +
526A ALA* 4.0 9.2 - - + -
527A MET* 1.3 77.3 - - - +
529A CYS* 1.3 60.6 + - - +
530A GLN* 5.6 1.3 - - + +
550A LYS 3.5 1.2 - - - +
551A ILE* 3.4 3.5 - - - -
552A THR* 2.6 50.2 + - + +
554A VAL* 4.7 1.1 - - + -
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Residues in contact with CYS 529 (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 GLY* 3.4 25.4 - - - +
432A VAL* 3.5 33.0 - - - -
433A CYS* 3.8 13.5 - - - -
498A GLU 3.9 0.5 - - - +
499A THR* 3.5 4.2 - - - -
500A TRP* 2.8 39.9 + - - +
527A MET* 4.2 7.4 - - - -
528A ILE* 1.3 81.6 - - - +
530A GLN* 1.3 64.1 + - - +
549A CYS* 3.6 5.4 - - - -
550A LYS 3.3 2.7 - - - -
551A ILE* 4.0 13.2 - - - -
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Residues in contact with GLN 530 (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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379A MET* 4.7 1.6 - - - +
383A LEU* 4.4 18.6 - - - +
429A GLY* 5.3 0.2 - - - -
497A PRO* 3.7 30.8 + - + +
498A GLU 3.5 13.7 - - - +
499A THR* 2.5 34.1 + - + +
528A ILE* 5.6 1.6 - - + -
529A CYS* 1.3 75.2 - - - +
531A THR* 1.3 61.4 + - - +
532A LEU* 4.0 5.6 + - + +
548A LEU 3.9 0.3 - - - +
549A CYS* 3.5 2.1 - - - -
550A LYS* 2.7 48.3 + - + +
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Residues in contact with THR 531 (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 VAL 4.4 2.9 - - - +
428A THR* 3.3 26.6 - - + -
429A GLY* 2.5 33.8 + - - -
430A HIS 4.6 0.2 + - - -
497A PRO* 4.1 12.5 - - - +
498A GLU 4.3 5.5 + - - -
500A TRP* 5.8 0.9 - - - -
530A GLN* 1.3 71.7 - - - +
532A LEU* 1.3 69.0 + - - +
533A VAL* 3.9 24.8 + - + +
547A ILE* 4.5 2.7 - - + -
548A LEU 3.6 6.7 - - - +
549A CYS* 4.5 0.8 - - - +
598A PHE* 4.7 4.5 - - + -
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Residues in contact with LEU 532 (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* 4.9 9.9 - - + -
530A GLN* 4.4 9.4 - - + +
531A THR* 1.3 77.9 - - - +
533A VAL* 1.3 63.2 + - - +
546A ASN 3.8 0.9 - - - +
547A ILE* 3.4 2.9 - - - +
548A LEU* 2.9 50.7 + - + +
550A LYS* 3.8 40.6 - - + -
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Residues in contact with VAL 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A THR* 3.9 13.1 + - + +
532A LEU* 1.3 78.1 - - - +
534A SER* 1.3 73.2 + - - +
542A ILE* 3.9 36.6 - - + -
546A ASN 3.3 6.3 - - - +
547A ILE* 3.6 9.0 - - + -
598A PHE* 3.5 29.2 - - + -
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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