Contacts of the strand formed by residues 516 - 521 (chain B) in PDB entry 4BL8
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 HIS 516 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B VAL 3.9 5.8 - - - +
502B SER* 3.4 0.8 - - - -
503B TRP* 3.1 20.9 + - - -
504B HIS* 3.2 46.8 + + - -
507B LEU* 3.6 3.8 - - - +
514B ILE 3.7 0.2 - - - -
515B GLN* 1.3 88.4 + - + +
517B MET* 1.3 75.7 + - - +
542B GLY* 3.3 5.5 - - - -
543B VAL* 3.1 34.9 + - + -
545B THR* 3.4 48.7 - - + +
548B LEU* 3.1 31.5 - - + +
549B HIS* 6.2 0.4 - - - -
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Residues in contact with MET 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 4.3 12.6 - - + -
484B LEU* 3.9 27.4 - - + -
500B HIS* 3.5 2.1 - - - +
501B VAL* 2.9 47.0 + - + +
503B TRP* 3.4 46.7 - - + -
507B LEU* 3.8 15.9 - - + -
516B HIS* 1.3 90.1 - - - +
518B LEU* 1.3 67.8 + - - +
519B LEU* 5.4 3.1 - - + -
540B ILE* 3.4 32.3 - - + -
541B VAL 3.4 5.8 - - - +
543B VAL* 3.7 1.7 - - - +
548B LEU* 4.9 0.7 - - - +
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Residues in contact with LEU 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B GLY 5.2 4.0 - - - +
499B ASP 3.6 5.6 - - - +
500B HIS* 3.5 28.3 - - + -
517B MET* 1.3 76.9 - - - +
519B LEU* 1.3 67.8 + - - +
539B GLN 3.7 0.3 - - - +
540B ILE* 3.8 0.2 - - - -
541B VAL* 2.9 41.9 + - + +
543B VAL* 3.9 27.1 - - + -
547B GLU* 5.1 4.9 - - + +
548B LEU* 4.7 6.7 - - + -
551B ALA* 3.7 26.7 - - + -
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Residues in contact with LEU 519 (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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458B PHE* 6.2 0.2 - - + -
460B LEU* 4.7 9.6 - - + -
484B LEU* 4.6 11.9 - - + -
495B PHE* 3.7 42.2 - - + -
496B CYS 4.3 9.6 - - - +
497B SER* 4.7 0.2 - - - -
498B GLY* 2.9 25.9 + - - -
499B ASP* 2.9 20.3 + - + +
501B VAL* 4.6 11.9 - - + -
517B MET* 5.4 2.9 - - + +
518B LEU* 1.3 83.0 - - - +
520B THR* 1.3 62.8 + - - +
538B LEU* 4.1 15.3 - - + -
539B GLN 3.5 12.3 - - - +
540B ILE* 4.0 23.3 - - + -
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Residues in contact with THR 520 (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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497B SER* 3.8 13.4 + - - +
498B GLY 4.5 0.2 - - - +
519B LEU* 1.3 75.1 - - - +
521B GLU* 1.3 69.9 + - - +
522B ASP 3.2 0.2 + - - -
523B PRO* 6.1 0.4 - - + -
538B LEU* 4.2 5.9 - - - +
539B GLN* 2.7 39.6 + - + +
541B VAL* 3.7 26.9 - - + -
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Residues in contact with GLU 521 (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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497B SER* 3.6 28.2 + - - +
520B THR* 1.3 85.1 + - - +
522B ASP* 1.3 69.2 + - - +
523B PRO* 3.2 6.8 - - - +
536B THR* 6.5 0.9 - - - -
537B PHE 3.7 7.9 - - - +
538B LEU* 4.4 5.4 - - + +
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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