Contacts of the strand formed by residues 561 - 573 (chain B) in PDB entry 5JMO
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460B ASP* 3.2 11.3 + - - +
461B ILE* 3.0 26.3 + - - -
462B GLY 4.5 3.0 - - - +
494B SER 3.2 12.8 - - - -
495B TYR* 3.7 5.6 - - - -
560B TYR* 1.3 77.6 - - - +
562B THR* 1.3 64.1 + - - -
33D SER* 3.8 6.5 + - - -
35D TYR* 3.2 12.3 - - - -
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Residues in contact with THR 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B PRO* 3.9 18.2 - - + -
459B LYS 3.5 16.2 - - - +
460B ASP* 4.9 0.3 + - - -
461B ILE* 3.6 5.4 - - - +
493B LEU* 3.2 2.6 - - - -
494B SER* 2.8 37.5 + - - -
561B GLY* 1.3 77.3 + - - -
563B LEU* 1.3 71.2 + - - +
564B THR* 3.7 9.8 + - + +
32D TYR* 4.3 9.9 - - + -
33D SER* 4.0 13.5 + - - -
35D TYR* 3.8 4.6 + - - -
98D VAL* 2.6 30.8 + - - +
99D GLY* 4.5 2.2 - - - -
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Residues in contact with LEU 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU* 3.7 20.0 - - + +
458B PRO* 3.3 3.5 - - - +
459B LYS* 2.9 40.9 + - + +
461B ILE* 3.7 8.0 - - + +
465B LEU* 3.9 26.2 - - + -
467B VAL* 4.4 9.0 - - + -
491B LEU* 4.4 12.1 - - + -
492B THR 3.3 19.3 - - - +
493B LEU* 4.0 8.5 - - + -
549B LEU* 4.1 13.9 - - + -
551B ILE* 4.1 20.9 - - + -
562B THR* 1.3 70.8 - - - +
564B THR* 1.3 59.3 + - - +
565B LYS 3.6 13.7 - - - +
566B PHE* 4.5 5.4 - - + -
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Residues in contact with THR 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU* 3.8 9.6 - - - +
457B GLU 5.7 0.2 - - - -
458B PRO* 4.2 16.8 - - + +
492B THR* 2.8 32.7 + - - +
493B LEU* 4.9 0.8 - - - -
494B SER* 5.4 0.7 - - - +
562B THR* 3.7 20.6 + - + +
563B LEU* 1.3 76.9 - - - +
565B LYS* 1.3 63.5 + - - +
98D VAL* 4.7 0.2 - - + -
99D GLY* 4.0 23.8 - - - +
101D TYR 4.2 7.1 + - - -
102D ALA* 4.2 19.3 - - + +
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Residues in contact with LYS 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B ASP* 3.6 25.0 + - - +
455B LEU* 3.8 8.0 - - + +
490B ARG 4.2 2.5 - - - +
491B LEU* 3.4 4.3 - - - -
492B THR* 2.9 48.7 + - + +
530B ASP* 4.7 12.6 - - - +
563B LEU* 3.6 7.2 - - - +
564B THR* 1.3 82.1 + - - +
566B PHE* 1.3 64.5 + - - +
567B THR* 3.8 17.2 + - - +
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Residues in contact with PHE 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B ASP* 3.8 3.2 - - - +
454B ILE* 2.9 68.8 + - + +
455B LEU* 4.0 18.9 + - + +
467B VAL* 4.2 12.3 - - + -
469B LYS* 6.0 0.4 - - + -
489B ALA* 3.9 21.1 - - + -
490B ARG 3.5 2.5 - - - -
491B LEU* 3.6 18.2 - - + -
505B LEU* 4.4 14.1 - - + -
547B TRP* 5.8 4.5 - - + -
549B LEU* 3.7 36.3 - - + -
563B LEU* 4.5 5.8 - - + -
565B LYS* 1.3 77.0 - - - +
567B THR* 1.3 71.8 + - - +
568B LEU* 4.2 10.5 - - + -
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Residues in contact with THR 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B ILE* 3.7 29.8 - - + -
452B ILE 3.5 6.5 - - - +
453B ASP* 3.2 23.5 + - - +
489B ALA* 3.6 2.9 - - - -
490B ARG* 2.9 50.8 + - - +
530B ASP* 5.2 0.7 + - - -
565B LYS* 3.8 15.2 + - - +
566B PHE* 1.3 73.9 - - - +
568B LEU* 1.3 62.2 + - - +
569B VAL* 3.7 13.6 + - + -
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Residues in contact with LEU 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B CYS 3.7 1.9 - - - +
451B ILE* 3.7 1.2 - - - -
452B ILE* 2.7 60.5 + - + +
454B ILE* 3.9 17.9 - - + +
471B VAL* 4.3 6.1 - - + -
487B ALA* 5.3 1.6 - - + -
488B GLN 3.6 14.1 - - - +
505B LEU* 4.5 11.7 - - + -
547B TRP* 3.7 54.5 - - + +
566B PHE* 4.2 15.5 - - + -
567B THR* 1.3 72.7 - - - +
569B VAL* 1.3 59.7 + - - +
570B LEU* 3.9 19.3 - - + -
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Residues in contact with VAL 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B LYS* 3.8 24.9 - - + -
450B CYS 3.5 4.5 - - - +
451B ILE* 4.6 8.1 - - + -
487B ALA* 3.5 4.9 - - - -
488B GLN* 2.9 54.5 + - + +
490B ARG* 4.1 20.6 - - + -
567B THR* 4.1 17.5 - - + -
568B LEU* 1.3 76.9 - - - +
570B LEU* 1.3 63.8 + - - +
571B TYR* 3.6 32.2 - - + +
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Residues in contact with LEU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LYS* 3.3 5.5 - - - +
450B CYS* 2.8 44.5 + - + +
452B ILE* 3.9 25.8 - - + -
471B VAL* 4.7 0.7 - - + -
473B ALA* 4.0 19.1 - - + -
481B ILE* 3.3 11.8 - - + +
484B LEU* 3.9 17.0 - - + -
487B ALA* 4.4 2.9 - - + -
543B PRO* 3.8 24.0 - - + +
547B TRP* 3.8 29.4 - - + +
568B LEU* 3.9 17.5 - - + -
569B VAL* 1.3 79.9 - - - +
571B TYR* 1.3 62.8 + - - +
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Residues in contact with TYR 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B ILE* 3.6 26.7 - - + +
313B TYR* 5.7 1.0 + - - -
447B GLN* 3.4 33.9 - - + +
448B ARG 3.3 10.3 - - - +
449B LYS* 3.7 36.3 + - + -
481B ILE* 3.9 4.0 - - - -
484B LEU* 3.3 9.7 - - - +
485B GLU* 2.7 30.3 + - + -
486B HIS* 3.1 38.3 + - + +
488B GLN* 3.1 38.3 + - + -
569B VAL* 3.6 14.8 - - + -
570B LEU* 1.3 74.8 - - - +
572B GLY* 1.3 53.5 + - - +
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Residues in contact with GLY 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B GLN* 3.9 1.5 - - - +
448B ARG* 2.9 35.3 + - - +
481B ILE* 3.8 9.6 - - - +
483B ARG 3.2 12.6 - - - -
485B GLU* 3.9 18.3 + - - -
571B TYR* 1.3 76.4 - - - +
573B THR* 1.3 67.0 + - - +
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Residues in contact with THR 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B ARG* 3.3 26.9 - - - +
444B VAL* 5.2 2.7 - - + -
445B ALA* 3.7 27.8 - - + +
446B PRO 3.8 6.1 - - - +
448B ARG* 4.4 7.4 - - - +
480B HIS 4.3 1.1 - - - -
481B ILE* 3.6 4.8 - - - +
482B THR 2.9 7.0 + - - -
483B ARG* 2.8 43.6 + - - +
485B GLU* 3.9 5.1 + - - +
572B GLY* 1.3 79.3 - - - +
574B ALA* 1.3 64.9 + - - +
575B SER* 4.6 3.8 - - - -
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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