Contacts of the strand formed by residues 469 - 478 (chain A) in PDB entry 1MDF
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 GLY 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A ASN* 4.2 11.2 - - - -
464A PRO* 3.9 4.0 - - - +
465A ASP 2.6 35.0 + - - +
466A GLN 4.4 1.9 + - - -
467A PHE 3.3 3.4 + - - -
468A LEU* 1.3 69.9 - - - +
470A GLU* 1.3 61.6 + - - +
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Residues in contact with GLU 470 (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 GLN 3.9 4.3 - - - +
433A ILE* 3.6 3.5 - - + -
434A ASN* 2.9 55.3 + - - +
435A ARG* 3.4 23.6 - - - +
462A SER* 3.4 36.2 + - - +
463A MET 3.4 12.1 - - - +
464A PRO* 4.9 0.9 - - + -
465A ASP* 3.9 4.0 - - - -
468A LEU* 2.9 13.7 + - - +
469A GLY* 1.3 77.3 - - - +
471A ARG* 1.3 60.1 + - - +
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Residues in contact with ARG 471 (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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433A ILE* 3.7 7.1 - - - +
435A ARG* 4.3 6.4 - - - +
462A SER* 3.3 7.1 - - - -
463A MET* 2.7 59.3 + - + +
464A PRO 4.7 0.9 - - - +
465A ASP* 2.8 37.0 + - + +
467A PHE* 5.5 3.8 - - - +
468A LEU* 3.3 30.7 - - - +
470A GLU* 1.3 74.2 - - - +
472A SER* 1.3 58.5 + - - +
504A ASP* 2.8 43.9 + - - +
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Residues in contact with SER 472 (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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433A ILE* 4.2 13.7 - - - -
435A ARG* 4.5 6.3 - - - +
440A VAL* 5.7 3.1 - - - -
460A MET* 4.1 18.5 - - - -
461A VAL 3.4 7.6 - - - -
463A MET* 3.9 2.1 - - - +
471A ARG* 1.3 76.0 - - - +
473A CYS* 1.3 60.4 + - - +
474A VAL 4.2 0.4 - - - -
500A TYR 5.4 0.2 + - - -
501A LYS 4.7 1.8 + - - -
502A ILE 3.9 4.2 + - - -
503A PRO* 3.3 8.5 - - - +
504A ASP* 3.0 30.6 + - - +
505A ARG* 2.9 23.4 + - - +
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Residues in contact with CYS 473 (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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460A MET* 4.2 1.3 - - - -
461A VAL* 2.8 37.1 + - + +
463A MET* 3.7 21.9 - - + +
472A SER* 1.3 74.1 - - - +
474A VAL* 1.3 61.6 + - - +
475A PHE* 3.7 23.6 + - + -
505A ARG* 3.5 13.2 - - + -
507A GLU* 3.7 19.3 - - - -
529A ILE* 3.4 32.5 - - + -
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Residues in contact with VAL 474 (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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446A GLU* 5.2 1.1 - - + -
449A LEU* 3.8 25.6 - - + -
458A ALA* 4.3 1.3 - - + -
459A ALA 3.8 5.4 - - - +
460A MET* 3.8 25.8 - - + +
472A SER 4.2 0.4 - - - -
473A CYS* 1.3 72.4 - - - +
475A PHE* 1.3 68.3 + - - +
476A ILE* 3.7 14.0 + - + -
488A LEU* 6.0 0.4 - - + -
503A PRO* 3.4 32.5 - - + +
505A ARG 2.9 13.9 + - - +
506A VAL* 3.5 16.0 - - + +
507A GLU 3.0 21.5 + - - +
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Residues in contact with PHE 475 (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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458A ALA* 3.3 4.7 - - - -
459A ALA 2.8 48.4 + - - +
461A VAL* 4.5 3.8 - - + -
473A CYS* 3.7 28.5 - - - -
474A VAL* 1.3 73.8 - - - +
476A ILE* 1.3 60.1 + - - +
507A GLU* 3.4 26.5 - - + -
509A VAL* 4.0 23.3 - - + -
512A PHE* 3.3 19.8 - - + -
525A LEU* 3.8 53.6 - - + -
528A ALA* 4.0 15.9 - - + -
529A ILE* 4.1 10.8 - - + -
532A LYS* 6.3 2.2 - - + -
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Residues in contact with ILE 476 (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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449A LEU* 3.6 22.4 - - + -
454A ALA 5.1 0.4 - - - +
455A VAL* 4.0 22.9 - - + -
457A ASP 3.6 4.5 - - - +
458A ALA* 3.4 27.8 - - + -
474A VAL* 3.8 13.5 - - + +
475A PHE* 1.3 73.6 - - - +
477A ILE* 1.3 74.1 + - - +
478A PRO* 3.6 3.1 - - + +
483A PRO* 5.4 0.4 - - + -
488A LEU* 3.8 20.0 - - + -
506A VAL* 4.2 6.1 - - + -
507A GLU 2.7 10.5 + - - +
508A PHE* 3.4 29.5 - - + -
509A VAL* 3.0 26.3 + - - +
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Residues in contact with ILE 477 (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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455A VAL* 3.7 1.9 - - - -
456A HIS* 2.7 58.5 + - + +
457A ASP* 2.9 21.8 + - + +
476A ILE* 1.3 73.7 - - - +
478A PRO* 1.3 65.7 - - + +
509A VAL 3.4 11.9 - - - +
510A GLU* 4.0 14.6 - - - +
511A SER* 3.6 24.9 - - - +
512A PHE* 3.5 39.9 - - + +
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Residues in contact with PRO 478 (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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454A ALA 3.5 9.4 - - - +
456A HIS* 3.6 7.7 - - - +
476A ILE* 3.6 7.2 - - + +
477A ILE* 1.3 92.9 - - + +
479A ARG* 1.3 60.6 + - - +
480A ASP 3.0 24.7 + - - +
481A GLU 4.3 0.4 - - - -
482A ALA* 3.7 34.3 - - + +
483A PRO* 5.0 0.4 - - + -
508A PHE* 3.9 13.0 - - + -
509A VAL 3.4 16.8 - - - +
510A GLU* 5.3 1.6 - - - -
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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