Contacts of the strand formed by residues 528 - 535 (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 PHE 528 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B VAL* 3.8 31.0 - - + -
305B CYS* 4.5 8.3 - - - -
491B LEU 4.0 8.1 - - - +
492B THR* 3.3 4.0 - - - -
493B LEU* 2.9 56.2 + - + +
498B ARG* 3.6 29.2 - - + -
501B LEU* 4.6 5.4 - - + -
503B ILE* 4.8 1.1 - - + -
516B LEU* 3.8 25.8 - - + -
519B ARG* 5.6 0.2 - - - -
522B ASP* 5.5 0.7 - - - -
526B ASP 3.6 0.2 + - - -
527B GLY* 1.3 76.8 - - - -
529B ASN* 1.3 60.4 + - - +
530B ASP 3.9 0.7 - - - -
531B TRP* 3.8 23.1 - + + -
533B PHE* 3.6 35.0 - + + -
101D TYR* 3.7 6.6 - - - -
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Residues in contact with ASN 529 (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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492B THR* 4.2 3.3 + - - +
527B GLY 4.4 0.2 - - - -
528B PHE* 1.3 72.0 - - - +
530B ASP* 1.3 77.4 + - - +
531B TRP* 3.2 7.3 + - - +
101D TYR* 3.7 48.2 - - + +
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Residues in contact with ASP 530 (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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490B ARG* 3.1 57.9 + - - +
491B LEU 3.0 9.8 + - - -
492B THR* 3.0 22.0 + - - +
529B ASN* 1.3 78.9 + - - +
531B TRP* 1.3 61.3 + - - +
565B LYS* 4.7 11.6 - - + +
567B THR* 5.2 1.0 + - - -
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Residues in contact with TRP 531 (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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263B VAL* 3.7 23.3 - - + +
264B ASP* 3.5 32.8 - - - -
265B GLY* 4.0 4.0 - - - -
304B ASN 2.9 28.3 + - - -
305B CYS* 3.8 10.6 - - - +
307B GLY* 3.7 24.9 - - - -
310B ASN* 3.9 11.2 - - - +
489B ALA 3.3 0.9 - - - +
490B ARG* 4.0 0.2 - - - -
491B LEU 2.9 26.1 + - - -
528B PHE* 3.8 26.9 - + + -
529B ASN 4.6 6.3 - - - +
530B ASP* 1.3 75.8 - - - +
532B ALA* 1.3 63.1 + - - +
533B PHE* 3.1 40.8 + + + -
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Residues in contact with ALA 532 (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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310B ASN* 2.3 32.1 + - - +
488B GLN* 3.8 19.8 + - + +
489B ALA 3.9 4.9 - - - -
490B ARG* 3.4 39.4 - - + +
530B ASP 3.7 2.8 + - - -
531B TRP* 1.3 76.0 - - - +
533B PHE* 1.3 56.6 + - - +
534B MET* 3.4 2.4 + - - +
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Residues in contact with PHE 533 (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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304B ASN* 4.0 13.2 - - + +
305B CYS* 5.2 0.2 - - - -
310B ASN* 3.9 3.6 - - - +
487B ALA 3.9 0.2 - - - +
488B GLN* 3.2 4.3 - - - -
489B ALA 2.8 42.7 + - - +
491B LEU* 3.8 29.8 - - + -
503B ILE* 4.3 8.7 - - + -
515B LEU* 3.3 51.7 - - + +
516B LEU* 3.9 14.6 - - + -
528B PHE* 3.6 42.0 - + - -
531B TRP* 3.1 30.1 + + - -
532B ALA* 1.3 69.9 - - - +
534B MET* 1.3 60.0 + - - +
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Residues in contact with MET 534 (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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304B ASN* 3.6 3.6 + - - +
310B ASN* 3.2 46.6 + - - +
311B SER 3.7 15.0 - - - +
312B ILE* 4.0 16.8 - - + -
314B THR 5.4 0.7 - - - +
334B SER* 2.7 22.6 + - - -
335B SER* 3.4 36.6 + - - +
486B HIS* 3.9 18.8 - - + -
487B ALA 3.4 10.3 - - - +
488B GLN* 4.1 9.0 - - + +
515B LEU* 4.6 1.6 - - - -
532B ALA 4.3 0.7 - - - +
533B PHE* 1.3 75.4 - - - +
535B THR* 1.3 86.7 + - - +
536B THR* 3.7 13.5 - - + -
606B NA 4.1 3.4 - - - -
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Residues in contact with THR 535 (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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334B SER* 3.4 16.2 - - - -
485B GLU 4.5 0.7 - - - +
486B HIS* 3.8 2.3 - - - -
487B ALA* 2.9 52.4 + - + +
505B LEU* 4.3 15.5 - - + -
513B SER* 2.8 35.5 + - - +
515B LEU* 4.3 3.4 - - + -
533B PHE 4.4 0.2 + - - -
534B MET* 1.3 80.4 - - - +
536B THR* 1.3 61.4 + - - +
537B HIS* 2.9 14.7 + - - +
538B SER* 5.1 7.7 + - - +
547B TRP* 5.6 1.8 - - + -
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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