Contacts of the strand formed by residues 506 - 517 (chain A) in PDB entry 3MXN
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 THR 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486A LEU* 4.2 13.7 - - + -
487A TYR* 4.1 18.6 - - - +
497A LEU* 3.8 29.8 - - + +
502A PRO* 3.6 14.5 - - + +
504A GLU* 2.9 20.0 + - - +
505A VAL* 1.3 73.4 + - - +
507A THR* 1.3 60.1 + - - +
508A VAL* 4.2 9.8 + - + +
594A ILE 3.7 1.6 - - - +
596A PHE* 2.8 41.6 + - - +
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Residues in contact with THR 507 (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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487A TYR* 3.5 25.8 + - - -
505A VAL* 4.5 3.5 + - - +
506A THR* 1.3 75.3 - - - +
508A VAL* 1.3 63.7 + - - +
593A THR* 3.6 28.5 - - + -
594A ILE 3.2 10.5 - - - +
595A SER* 3.8 15.9 + - - -
606A LEU* 4.3 11.2 - - + +
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Residues in contact with VAL 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A LEU* 3.5 29.4 - - + +
487A TYR* 5.5 0.4 - - - -
492A VAL* 3.7 14.6 - - + -
493A TYR 6.1 0.2 - - - +
494A LEU* 4.8 4.3 - - + -
497A LEU* 4.0 29.6 - - + -
506A THR* 4.3 18.6 - - + +
507A THR* 1.3 78.5 - - - +
509A LYS* 1.3 59.3 + - - +
510A VAL* 4.1 19.0 + - + -
592A MET 3.6 1.0 - - - +
593A THR* 3.5 3.6 - - - +
594A ILE* 2.8 40.3 + - + +
596A PHE* 6.1 0.4 - - + -
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Residues in contact with LYS 509 (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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486A LEU 5.0 0.4 + - - -
490A PRO 3.5 23.2 + - - +
491A PHE* 3.3 3.9 - - + -
492A VAL* 2.8 30.3 + - - +
508A VAL* 1.3 75.2 - - - +
510A VAL* 1.3 62.9 + - - +
591A LEU* 3.7 25.4 - - + +
592A MET 3.4 10.1 - - - +
593A THR* 3.9 20.0 - - + +
609A GLN* 3.0 28.0 + - - +
615A HIS* 4.5 4.2 + - - -
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Residues in contact with VAL 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A PHE* 3.9 4.7 - - - -
492A VAL* 3.4 23.8 - - + +
493A TYR 4.7 0.2 - - - -
494A LEU* 3.9 29.6 - - + +
508A VAL* 4.1 14.1 - - + -
509A LYS* 1.3 78.8 - - - +
511A LYS* 1.3 59.3 + - - +
512A ALA* 3.7 18.1 + - + -
536A ASP* 4.3 11.0 - - + +
590A CYS 3.5 0.2 - - - +
591A LEU* 3.3 3.5 - - - -
592A MET* 2.7 36.7 + - + +
594A ILE* 3.7 28.5 - - + -
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Residues in contact with LYS 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A PHE* 3.9 28.2 - - + +
492A VAL 4.8 0.2 + - - -
510A VAL* 1.3 70.9 - - - +
512A ALA* 1.3 61.5 + - - +
536A ASP* 3.3 24.3 - - - +
589A CYS* 4.0 18.1 - - - -
590A CYS 3.4 11.7 - - - +
591A LEU* 3.6 14.4 - - + -
611A VAL* 3.8 24.4 - - + +
24B LYS* 4.8 4.8 + - - +
59B TRP* 4.0 11.6 - - + -
61B GLN* 5.0 5.1 + - - +
131B HIS* 3.0 39.8 + - - +
134B MET* 4.5 2.0 - - + +
138B GLU* 3.1 39.0 + - - +
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Residues in contact with ALA 512 (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 LEU* 5.8 0.2 - - + -
510A VAL* 3.7 15.7 + - + -
511A LYS* 1.3 75.8 - - - +
513A PHE* 1.3 63.2 - - - +
534A VAL* 4.4 6.7 - - + -
535A SER 3.2 20.9 - - - +
536A ASP* 4.2 0.9 - - - +
589A CYS* 3.4 3.7 - - - -
590A CYS 3.0 30.5 + - - +
592A MET* 3.6 29.3 - - + +
59B TRP* 4.5 4.5 - - - -
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Residues in contact with PHE 513 (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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512A ALA* 1.3 73.4 - - - +
514A ILE* 1.3 74.9 + - - +
515A VAL* 3.6 21.0 + - + -
534A VAL* 3.2 6.2 - - - +
535A SER* 3.0 43.1 + - - -
588A LEU 3.3 19.5 - - - +
589A CYS* 4.5 8.7 - - + -
592A MET* 4.4 2.5 - - - -
22B PRO* 4.0 13.5 - - + -
59B TRP* 3.5 32.5 - + - -
103B MET* 3.6 31.0 - - + -
105B MET* 3.7 30.1 - - + -
121B LYS* 4.0 16.6 - - + +
123B THR* 6.1 0.9 - - - +
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Residues in contact with ILE 514 (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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513A PHE* 1.3 75.2 - - - +
515A VAL* 1.3 64.7 + - - +
516A THR* 3.6 29.4 - - - +
517A LEU* 4.1 9.0 - - + +
532A ALA* 3.9 7.9 - - + -
533A LYS 3.7 5.4 - - - +
534A VAL* 4.0 16.2 - - + +
545A PHE* 3.8 25.6 - - + -
585A LEU* 3.6 47.6 - - + +
588A LEU* 3.9 15.8 + - + -
592A MET* 4.6 1.1 - - + -
121B LYS* 2.8 31.3 + - - +
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Residues in contact with VAL 515 (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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513A PHE* 3.7 23.8 - - + -
514A ILE* 1.3 74.1 - - - +
516A THR* 1.3 66.5 + - + +
533A LYS* 2.8 24.9 + - + +
535A SER* 3.9 17.7 - - - +
540A TYR* 3.8 28.9 - - + -
17B LEU 5.6 6.3 - - - +
90B PRO* 5.8 1.9 - - - +
105B MET* 4.0 23.3 - - + -
120B VAL* 5.0 8.1 - - + +
121B LYS* 3.9 14.1 - - - +
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Residues in contact with THR 516 (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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514A ILE* 3.5 9.9 - - - +
515A VAL* 1.3 86.7 - - + +
517A LEU* 1.3 74.2 + - - +
518A THR* 4.1 12.8 - - + -
532A ALA* 3.5 1.6 - - - -
533A LYS* 2.8 43.4 + - + -
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Residues in contact with LEU 517 (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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514A ILE* 4.1 11.4 - - + +
516A THR* 1.3 90.9 + - - +
518A THR* 1.3 59.5 + - - +
519A GLY 3.6 9.6 - - - +
530A ILE* 4.0 28.9 - - + -
531A THR 3.7 5.2 - - - +
532A ALA* 4.0 17.5 - - + -
582A GLN* 6.0 8.5 - - + -
585A LEU* 4.3 24.5 - - + -
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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