Contacts of the strand formed by residues 518 - 522 (chain B) in PDB entry 1F89
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 TYR 518 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B LEU* 5.1 0.4 - - + -
487B PHE 2.8 16.0 + - - +
488B ALA* 2.9 13.0 - - + -
489B MET 2.8 25.6 + - - -
517B VAL* 1.3 73.0 - - - +
519B VAL* 1.3 62.9 + - - +
520B MET* 4.9 2.2 - - + -
540B VAL* 4.5 7.2 - - + -
541B VAL 3.4 16.4 - - - -
542B ASP* 3.5 22.2 - - + +
543B PRO* 3.5 6.5 - - + -
548B VAL* 5.2 4.5 - - + -
561B GLU 4.1 5.2 + - - -
562B LEU* 3.7 46.8 - - + -
563B ASP 3.2 17.1 + - - -
566B VAL* 3.4 23.4 - - - +
567B ILE* 3.5 39.5 - - + -
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Residues in contact with VAL 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B MET* 3.4 16.4 - - + +
491B TYR* 4.3 7.9 - - + -
508B ALA* 3.7 23.8 - - + +
511B ARG* 4.0 10.1 - - + +
512B ALA* 3.5 32.1 - - + +
517B VAL* 3.9 5.6 + - + -
518B TYR* 1.3 79.9 - - - +
520B MET* 1.3 64.4 + - - +
521B LEU* 3.8 24.5 - - + -
539B ILE* 3.7 2.1 - - - +
540B VAL* 3.3 4.0 - - - +
541B VAL* 3.0 38.1 + - + +
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Residues in contact with MET 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B VAL* 4.0 26.5 - - + -
315B LEU* 4.2 21.1 - - + -
348B LEU* 4.7 3.1 - - + -
350B VAL* 4.8 2.0 - - - -
487B PHE* 5.3 0.2 - - + -
488B ALA* 4.1 14.8 - - + -
489B MET 3.2 5.5 + - - +
490B ILE* 3.5 37.2 - - + +
491B TYR 2.9 26.3 + - - -
518B TYR* 4.9 0.2 - - + -
519B VAL* 1.3 79.1 - - - +
521B LEU* 1.3 66.4 + - - +
522B CYS 4.2 0.2 - - - -
539B ILE 3.2 5.8 - - - +
540B VAL* 3.8 17.0 - - + -
562B LEU* 3.6 39.5 - - + -
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Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 3.5 4.1 - - - +
472B MET* 3.4 32.3 - - + -
491B TYR* 3.6 34.3 - - + +
504B TRP* 3.5 41.3 - - + +
508B ALA* 3.5 25.1 - - + -
519B VAL* 3.8 9.9 - - + -
520B MET* 1.3 84.7 - - - +
522B CYS* 1.3 60.7 + - - +
523B SER 3.9 0.4 - - - -
538B SER* 3.0 7.5 - - - -
539B ILE* 2.9 36.3 + - + -
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Residues in contact with CYS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 4.3 7.9 - - + -
316B VAL 3.7 23.6 - - - -
350B VAL* 3.6 31.0 - - + -
351B LEU 3.2 31.6 - - - +
352B PRO* 3.2 16.0 - - - +
490B ILE* 6.0 0.2 - - - +
491B TYR 3.2 8.5 + - - -
492B PRO* 3.7 4.2 - - + +
493B SER 3.0 23.1 + - - +
504B TRP* 4.7 0.7 - - - -
520B MET 4.2 0.6 - - - -
521B LEU* 1.3 73.0 - - - +
523B SER* 1.3 59.0 + - - +
538B SER* 3.5 5.8 - - - -
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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
------------------------------------------------------------
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