Contacts of the strand formed by residues 561 - 573 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460C ASP* 3.3 9.7 + - - +
461C ILE* 3.0 27.5 + - - +
462C GLY 4.7 1.6 - - - +
494C SER* 3.0 18.8 - - - -
495C TYR* 3.7 8.1 - - - -
560C TYR* 1.3 78.9 - - - +
562C THR* 1.3 66.0 + - - -
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Residues in contact with THR 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458C PRO* 3.9 20.2 - - + -
459C LYS 3.3 15.3 - - - +
460C ASP* 4.1 7.9 + - - +
461C ILE* 4.0 4.5 - - - -
493C LEU* 3.2 3.3 - - - -
494C SER* 2.9 40.0 + - - -
561C GLY* 1.3 78.7 + - - -
563C LEU* 1.3 71.0 + - - +
564C THR* 3.6 14.6 + - + +
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Residues in contact with LEU 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455C LEU* 3.6 19.8 - - + +
458C PRO* 3.5 2.3 - - - +
459C LYS* 2.8 37.6 + - + +
461C ILE* 3.9 6.7 - - + +
465C LEU* 3.8 26.9 - - + -
467C VAL* 4.3 9.9 - - + -
491C LEU* 4.5 9.4 - - + -
492C THR 3.6 10.8 - - - +
493C LEU* 3.9 10.8 - - + -
549C LEU* 4.1 15.9 - - + -
551C ILE* 4.0 18.4 - - + -
562C THR* 1.3 71.4 - - - +
564C THR* 1.3 58.4 + - - +
565C LYS 3.3 25.1 - - - +
566C PHE* 4.4 5.6 - - + -
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Residues in contact with THR 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455C LEU* 3.7 12.6 - - - +
457C GLU 5.6 0.3 - - - -
458C PRO* 4.5 19.0 - - + +
492C THR* 2.9 31.4 + - - +
493C LEU* 4.9 0.8 - - - -
494C SER* 5.7 1.8 - - - +
562C THR* 3.6 23.8 + - + +
563C LEU* 1.3 76.4 - - - +
565C LYS* 1.3 62.8 + - - +
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Residues in contact with LYS 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453C ASP* 4.1 10.1 - - - +
455C LEU* 3.9 4.9 - - - -
490C ARG* 3.4 21.3 + - - +
491C LEU* 3.3 4.9 - - - -
492C THR* 2.8 59.5 + - - +
530C ASP* 2.9 29.8 + - - -
563C LEU* 3.3 10.2 - - - +
564C THR* 1.3 82.2 - - - +
566C PHE* 1.3 65.0 + - - +
567C THR* 3.6 22.7 - - - +
232D THR* 6.2 3.6 - - - -
233D ASP* 5.8 11.2 - - + -
269D LEU* 6.1 2.5 - - - -
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Residues in contact with PHE 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453C ASP* 3.7 1.8 + - - +
454C ILE* 3.0 64.1 + - + +
455C LEU* 4.0 18.5 - - + +
467C VAL* 4.2 13.9 - - + -
469C LYS* 5.8 1.8 - - + -
489C ALA* 4.0 23.8 - - + -
490C ARG 3.4 2.7 - - - -
491C LEU* 3.3 20.0 - - + -
505C LEU* 4.3 12.1 - - + -
547C TRP* 5.7 6.5 - - + -
549C LEU* 3.7 41.7 - - + -
563C LEU* 4.4 2.7 - - + -
565C LYS* 1.3 77.3 - - - +
567C THR* 1.3 67.4 + - - +
568C LEU* 4.6 10.8 - - + -
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Residues in contact with THR 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451C ILE* 3.7 29.8 - - + -
452C ILE 3.6 9.9 - - - +
453C ASP* 2.8 20.9 + - - +
488C GLN 3.6 0.7 - - - +
489C ALA* 3.6 1.7 - - - -
490C ARG* 2.8 51.5 + - - +
565C LYS* 3.6 18.0 - - - +
566C PHE* 1.3 75.0 - - - +
568C LEU* 1.3 65.8 + - - +
569C VAL* 4.2 4.5 - - + -
234D ALA* 4.6 4.0 - - + +
269D LEU* 4.0 13.9 - - + +
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Residues in contact with LEU 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C CYS 3.7 1.7 - - - +
451C ILE 3.7 0.3 - - - -
452C ILE* 2.8 59.0 + - + +
454C ILE* 4.5 12.3 - - + +
471C VAL* 4.5 5.4 - - + -
487C ALA* 5.3 1.3 - - + -
488C GLN 3.5 15.3 - - - +
489C ALA* 4.8 0.2 - - - -
505C LEU* 4.3 22.2 - - + -
547C TRP* 3.7 47.3 - - + +
566C PHE* 4.0 15.1 + - + -
567C THR* 1.3 71.9 - - - +
569C VAL* 1.3 61.6 + - - +
570C LEU* 3.9 20.2 - - + -
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Residues in contact with VAL 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449C LYS* 3.8 28.0 - - + -
450C CYS 3.6 4.5 - - - +
451C ILE* 4.6 6.1 - - + -
486C HIS 4.2 0.2 - - - +
487C ALA* 3.3 5.4 - - - -
488C GLN* 2.8 50.5 + - + +
490C ARG* 4.1 28.5 - - + -
567C THR* 4.2 9.9 - - + -
568C LEU* 1.3 77.0 - - - +
570C LEU* 1.3 66.0 + - - +
571C TYR* 3.6 24.9 + - + -
269D LEU* 4.2 11.2 - - + -
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Residues in contact with LEU 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449C LYS* 3.2 5.5 - - - +
450C CYS* 2.7 45.9 + - + +
452C ILE* 3.8 25.8 - - + -
471C VAL* 4.9 3.4 - - + -
473C ALA* 4.1 17.3 - - + -
481C ILE* 3.3 10.4 - - + +
484C LEU* 3.8 23.1 - - + -
486C HIS 4.2 0.4 - - - -
487C ALA* 4.4 4.7 - - + -
543C PRO* 3.8 20.4 - - + +
547C TRP* 4.0 18.4 - - + -
568C LEU* 3.9 23.3 - - + -
569C VAL* 1.3 77.0 - - - +
571C TYR* 1.3 62.5 + - - +
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Residues in contact with TYR 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C ILE* 3.8 22.3 - - + +
447C GLN* 3.7 27.8 - - + +
448C ARG 3.3 4.9 - - - +
449C LYS* 3.4 41.7 + - + -
481C ILE* 3.4 2.9 - - - -
484C LEU* 3.3 8.5 - - - +
485C GLU* 2.9 24.4 + - + -
486C HIS* 3.1 40.9 + - + +
487C ALA 4.7 0.2 - - - -
488C GLN* 3.3 32.1 + - + -
569C VAL* 3.6 20.9 - - + -
570C LEU* 1.3 75.3 - - - +
572C GLY* 1.3 59.3 + - - +
602C FMT 3.6 17.7 - - - -
272D GLU* 4.2 4.7 + - - -
276D ARG* 4.2 2.5 - - - -
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Residues in contact with GLY 572 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C ARG* 4.8 0.2 - - - -
447C GLN* 4.6 1.0 - - - +
448C ARG* 2.8 42.0 + - - +
481C ILE* 3.4 8.7 - - - +
483C ARG 3.3 10.3 - - - -
485C GLU* 4.0 19.5 + - - -
571C TYR* 1.3 75.6 - - - +
573C THR* 1.3 67.3 + - - +
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Residues in contact with THR 573 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C ARG* 3.3 29.4 - - - +
395C HIS* 6.1 0.5 - - - -
444C VAL* 5.1 2.9 - - + -
445C ALA* 3.5 28.0 - - + +
446C PRO 3.7 6.5 - - - +
448C ARG* 4.4 6.3 - - - +
480C HIS 4.4 3.8 - - - -
481C ILE* 3.6 1.9 - - - -
482C THR 3.0 22.0 + - - -
483C ARG* 3.0 34.7 + - - +
485C GLU* 4.2 4.6 + - - +
572C GLY* 1.3 76.2 - - - +
574C ALA* 1.3 67.9 + - - +
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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