Contacts of the strand formed by residues 501 - 506 (chain A) in PDB entry 5JXH
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A ILE* 4.4 2.0 - - + -
493A LEU* 3.8 32.3 - - + -
495A TYR* 3.5 48.5 - - + +
498A ARG* 3.0 20.0 + - + +
499A GLY 4.1 1.2 - - - +
500A ASP* 1.3 79.8 - - - +
502A ALA* 1.3 59.7 + - - +
503A ILE* 4.7 7.2 - - + -
516A LEU* 3.9 15.1 - - + +
517A ALA 3.8 5.0 - - - +
518A ALA* 3.7 17.7 + - - -
528A PHE* 4.6 11.4 - - + -
551A ILE* 3.8 23.6 - - + -
552A GLU 3.4 7.6 - - - +
554A THR* 4.6 0.7 - - - -
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Residues in contact with ALA 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500A ASP 3.7 0.2 + - - -
501A LEU* 1.3 73.5 - - - +
503A ILE* 1.3 64.7 + - - +
504A HIS* 4.3 15.8 + - + -
516A LEU 3.2 10.5 - - - +
517A ALA* 4.5 2.0 - - - -
518A ALA 4.3 7.6 - - - +
550A GLU 3.8 0.5 - - - +
551A ILE* 3.6 1.0 - - - +
552A GLU* 2.9 43.4 + - + +
554A THR* 3.6 22.0 - - + -
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Residues in contact with ILE 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A LEU* 4.0 22.0 - - + -
493A LEU* 4.4 15.7 - - + -
501A LEU* 4.7 4.3 - - + -
502A ALA* 1.3 81.5 - - - +
504A HIS* 1.3 66.8 + - - +
514A THR 3.6 1.6 - - - -
515A LEU* 2.8 36.7 + - + -
516A LEU* 2.7 47.4 + - + +
528A PHE* 4.7 2.2 - - + -
533A PHE* 4.2 12.3 - - + -
549A LEU* 3.7 22.9 - - + -
550A GLU 3.2 10.5 - - - +
551A ILE* 4.2 15.7 - - + -
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Residues in contact with HIS 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A ALA* 4.3 16.3 + - + -
503A ILE* 1.3 80.7 + - - +
505A LEU* 1.3 60.3 + - - +
506A VAL* 5.2 0.2 - - - -
512A ARG* 3.1 48.9 + - + +
513A SER 3.3 5.8 - - - +
514A THR* 3.3 38.0 + - + +
515A LEU* 4.3 1.8 - - - +
548A VAL 3.8 0.6 - - - +
549A LEU* 3.5 8.5 - - - +
550A GLU* 2.8 51.3 + - - +
552A GLU* 4.1 15.6 + - - -
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Residues in contact with LEU 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A ALA* 5.2 2.0 - - + -
488A GLN 5.2 0.2 - - - -
489A ALA* 4.4 15.5 - - + +
504A HIS* 1.3 74.4 - - - +
506A VAL* 1.3 61.9 + - - +
507A SER 4.1 0.2 + - - -
511A THR 3.4 2.6 - - - +
513A SER* 2.8 40.8 + - - +
515A LEU* 3.6 20.6 - - + +
535A THR* 4.5 17.9 - - + -
547A TRP* 3.7 37.7 - - + -
548A VAL 3.3 17.7 - - - +
549A LEU* 4.2 7.4 - - + -
566A PHE* 4.2 24.7 - - + -
568A LEU* 4.3 11.9 - - + -
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Residues in contact with VAL 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505A LEU* 1.3 77.8 - - - +
507A SER* 1.3 72.1 + - - +
510A GLY* 4.0 17.7 - - - +
511A THR 3.4 9.4 - - - +
512A ARG* 4.0 23.8 - - + +
546A GLU 4.0 0.3 - - - +
547A TRP* 3.4 10.5 - - - -
548A VAL* 2.8 52.9 + - + +
550A GLU* 4.1 20.6 - - - +
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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