Contacts of the strand formed by residues 561 - 573 (chain D) in PDB entry 4OMD
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 561 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460D ASP* 3.4 11.1 + - - +
461D ILE* 3.0 26.9 + - - +
462D GLY 4.7 1.6 - - - +
494D SER* 3.0 17.7 - - - -
495D TYR* 3.7 7.7 - - - -
560D TYR* 1.3 79.6 - - - +
562D THR* 1.3 66.6 + - - -
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Residues in contact with THR 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D PRO* 3.9 20.6 - - + -
459D LYS 3.2 15.5 - - - +
460D ASP* 4.1 8.5 + - - -
461D ILE* 3.9 5.4 - - - +
493D LEU* 3.2 3.1 - - - -
494D SER* 2.9 40.2 + - - -
561D GLY* 1.3 76.9 + - - -
563D LEU* 1.3 71.4 + - - +
564D THR* 3.7 14.6 + - + +
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Residues in contact with LEU 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D LEU* 3.6 22.2 - - + +
458D PRO* 3.5 2.1 - - - +
459D LYS* 2.8 39.6 + - + +
461D ILE* 4.0 4.0 - - + +
465D LEU* 3.7 28.7 - - + -
467D VAL* 4.3 9.4 - - + -
491D LEU* 4.5 10.5 - - + -
492D THR 3.7 9.9 - - - +
493D LEU* 3.9 15.7 - - + -
549D LEU* 4.1 14.6 - - + -
551D ILE* 3.9 20.4 - - + -
562D THR* 1.3 71.4 - - - +
564D THR* 1.3 58.2 + - - +
565D LYS 3.6 20.4 - - - +
566D PHE* 4.4 4.3 - - + -
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Residues in contact with THR 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D LEU* 3.7 12.3 - - - +
457D GLU 5.6 0.5 - - - -
458D PRO* 4.4 18.1 - - + +
492D THR* 2.8 32.1 + - - +
493D LEU* 4.8 0.6 - - - -
494D SER* 5.7 1.6 - - - +
562D THR* 3.7 22.6 + - + +
563D LEU* 1.3 78.1 - - - +
565D LYS* 1.3 62.6 + - - +
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Residues in contact with LYS 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C THR* 6.4 2.2 - - - -
233C ASP* 6.0 9.4 - - + -
269C LEU* 6.1 2.5 - - - -
453D ASP* 4.2 10.3 - - - +
455D LEU* 3.7 6.5 - - - +
490D ARG* 3.3 23.3 + - - +
491D LEU* 3.3 4.9 - - - -
492D THR* 2.8 60.4 + - - +
530D ASP* 3.1 29.0 + - - +
563D LEU* 3.6 7.0 - - - +
564D THR* 1.3 80.9 - - - +
566D PHE* 1.3 64.3 + - - +
567D THR* 3.6 21.3 - - - +
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Residues in contact with PHE 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D ASP* 3.7 2.0 + - - +
454D ILE* 3.0 63.6 + - + +
455D LEU* 4.0 16.6 + - + +
467D VAL* 4.2 14.8 - - + -
469D LYS* 5.8 1.6 - - + -
489D ALA* 3.9 24.7 - - + -
490D ARG 3.4 2.2 - - - -
491D LEU* 3.2 21.1 - - + -
505D LEU* 4.2 14.4 - - + -
547D TRP* 5.7 6.7 - - + -
548D VAL 5.6 0.4 - - - -
549D LEU* 3.8 39.3 - - + -
563D LEU* 4.4 4.3 - - + -
565D LYS* 1.3 77.5 - - - +
567D THR* 1.3 68.2 + - - +
568D LEU* 4.7 9.9 - - + -
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Residues in contact with THR 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ALA* 4.5 1.7 - - + +
269C LEU* 4.1 13.7 - - + +
451D ILE* 3.7 30.3 - - + -
452D ILE 3.6 10.8 - - - +
453D ASP* 2.9 21.6 + - - +
488D GLN 3.7 0.5 - - - +
489D ALA* 3.6 2.3 - - - -
490D ARG* 2.8 50.3 + - - +
565D LYS* 3.6 19.8 - - - +
566D PHE* 1.3 74.2 - - - +
568D LEU* 1.3 63.7 + - - +
569D VAL* 3.8 5.0 + - + -
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Residues in contact with LEU 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D CYS 3.7 2.4 - - - +
452D ILE* 2.8 61.5 + - + +
454D ILE* 4.4 11.7 - - + -
471D VAL* 4.4 6.3 - - + -
487D ALA* 5.3 1.1 - - + -
488D GLN 3.5 15.0 - - - +
489D ALA* 4.8 0.7 - - - +
505D LEU* 4.5 16.8 - - + -
547D TRP* 3.8 55.9 - - + +
566D PHE* 4.0 8.8 + - + -
567D THR* 1.3 72.3 - - - +
569D VAL* 1.3 61.8 + - - +
570D LEU* 3.8 21.8 - - + -
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Residues in contact with VAL 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C LEU* 4.2 11.7 - - + -
449D LYS* 3.8 28.9 - - + -
450D CYS 3.6 4.3 - - - +
451D ILE* 4.6 5.6 - - + -
487D ALA* 3.4 5.0 - - - -
488D GLN* 2.9 50.4 + - + +
490D ARG* 4.0 30.3 - - + -
567D THR* 4.3 8.1 - - + -
568D LEU* 1.3 78.7 - - - +
570D LEU* 1.3 64.0 + - - +
571D TYR* 3.6 25.3 + - + -
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Residues in contact with LEU 570 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449D LYS* 3.3 4.5 - - - +
450D CYS* 2.7 45.6 + - + +
452D ILE* 3.8 25.8 - - + -
471D VAL* 4.9 2.7 - - + -
473D ALA* 4.0 17.9 - - + -
481D ILE* 3.2 14.2 - - + +
484D LEU* 3.8 16.6 - - + -
487D ALA* 4.6 2.9 - - + -
543D PRO* 3.8 19.3 - - + -
547D TRP* 3.9 24.2 - - + -
568D LEU* 3.8 24.0 - - + -
569D VAL* 1.3 76.9 - - - +
571D TYR* 1.3 62.0 + - - +
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Residues in contact with TYR 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C GLU* 4.1 3.8 + - - -
276C ARG* 4.4 1.1 - - - -
312D ILE* 3.8 23.7 - - + +
447D GLN* 3.6 29.6 - - + +
448D ARG 3.2 6.5 - - - -
449D LYS* 3.6 30.0 + - + -
481D ILE* 3.6 3.3 - - - +
484D LEU* 3.3 8.3 - - - +
485D GLU* 2.8 24.9 + - + +
486D HIS* 3.1 39.9 + - + +
488D GLN* 3.2 38.2 + - + -
569D VAL* 3.6 16.4 - - + -
570D LEU* 1.3 76.7 - - - +
572D GLY* 1.3 60.0 + - - +
602D FMT 3.7 25.7 - - - -
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Residues in contact with GLY 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D GLN* 3.8 1.9 - - - +
448D ARG* 2.8 42.5 + - - +
481D ILE* 3.6 6.6 - - - +
483D ARG 3.4 10.1 - - - -
485D GLU* 4.0 19.0 + - - -
571D TYR* 1.3 77.1 - - - +
573D THR* 1.3 66.7 + - - +
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Residues in contact with THR 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D ARG* 3.5 25.1 - - - +
395D HIS* 6.1 0.7 - - - -
444D VAL* 5.1 2.5 - - + -
445D ALA* 3.7 28.0 - - + +
446D PRO 3.9 5.6 - - - +
448D ARG* 4.6 5.2 - - - +
480D HIS 4.3 1.3 - - - -
481D ILE* 3.4 5.3 - - - -
482D THR 2.8 22.5 + - - -
483D ARG* 3.0 37.0 + - - +
485D GLU* 4.2 5.4 + - - +
572D GLY* 1.3 78.9 - - - +
574D ALA* 1.3 66.5 + - - +
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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