Contacts of the strand formed by residues 501 - 506 (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 LEU 501 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B ILE* 4.5 1.3 - - + -
493B LEU* 3.6 35.7 - - + -
495B TYR* 3.7 46.7 - - + -
498B ARG* 3.0 21.0 + - + +
499B GLY 4.1 1.0 - - - +
500B ASP* 1.3 79.7 - - - +
502B ALA* 1.3 59.5 + - - +
503B ILE* 4.7 5.4 - - + -
516B LEU* 4.1 15.2 - - + +
517B ALA 3.7 5.0 - - - +
518B ALA* 3.7 18.7 + - - -
519B ARG 4.9 0.2 + - - -
528B PHE* 4.6 9.9 - - + -
551B ILE* 3.7 26.0 - - + -
552B GLU 3.4 7.4 - - - +
554B THR* 4.4 1.1 - - - -
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Residues in contact with ALA 502 (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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500B ASP 3.8 0.4 + - - -
501B LEU* 1.3 72.5 - - - +
503B ILE* 1.3 63.6 + - - +
504B HIS* 4.2 12.3 + - + -
516B LEU 3.2 11.4 - - - +
517B ALA* 4.6 2.0 - - - -
518B ALA 4.5 6.3 - - - +
550B GLU 3.8 0.9 - - - +
551B ILE* 3.5 2.8 - - - +
552B GLU* 2.8 48.5 + - + +
554B THR* 3.6 21.5 - - + -
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Residues in contact with ILE 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B LEU* 3.9 25.1 - - + -
493B LEU* 4.1 18.8 - - + -
501B LEU* 4.7 4.9 - - + -
502B ALA* 1.3 79.4 - - - +
504B HIS* 1.3 68.6 + - - +
514B THR* 3.6 1.0 - - - -
515B LEU* 2.8 34.9 + - + -
516B LEU* 2.8 42.9 + - + +
528B PHE* 4.8 1.6 - - + -
533B PHE* 4.3 11.4 - - + -
549B LEU* 3.8 22.9 - - + -
550B GLU 3.2 10.1 - - - +
551B ILE* 4.2 16.4 - - + -
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Residues in contact with HIS 504 (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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502B ALA* 4.2 21.2 + - + -
503B ILE* 1.3 80.7 + - - +
505B LEU* 1.3 61.5 + - - +
506B VAL* 4.3 0.7 - - + -
512B ARG* 3.4 37.9 + - + +
513B SER 3.2 6.7 - - - +
514B THR* 3.1 39.5 + - + +
515B LEU* 4.6 1.6 - - - -
549B LEU* 3.5 9.2 - - - +
550B GLU* 2.8 47.7 + - + +
552B GLU* 4.4 13.1 + - - -
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Residues in contact with LEU 505 (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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487B ALA* 5.0 3.4 - - + -
488B GLN 5.3 0.2 - - - -
489B ALA* 4.4 18.8 - - + +
504B HIS* 1.3 73.5 - - - +
506B VAL* 1.3 60.5 + - - +
511B THR 3.3 2.3 - - - +
512B ARG* 4.5 0.2 - - - -
513B SER* 2.7 43.6 + - - +
515B LEU* 3.9 20.6 - - + +
535B THR* 4.3 19.3 - - + -
547B TRP* 3.7 37.9 - - + -
548B VAL 3.4 18.4 - - - +
549B LEU* 4.3 13.2 - - + -
566B PHE* 4.4 14.8 - - + -
568B LEU* 4.5 8.1 - - + -
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Residues in contact with VAL 506 (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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505B LEU* 1.3 77.8 - - - +
507B SER* 1.3 73.8 + - - +
510B GLY* 4.0 16.8 - - - +
511B THR 3.3 7.9 - - - +
512B ARG* 3.6 38.1 - - + +
546B GLU 4.1 0.3 - - - +
547B TRP* 3.4 10.0 - - - -
548B VAL* 2.8 56.1 + - + +
550B GLU* 3.9 11.4 - - - +
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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