Contacts of the strand formed by residues 572 - 577 (chain B) in PDB entry 5FLM
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 CYS 572 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350B HIS* 3.9 35.1 - - + +
351B VAL* 4.4 18.8 - - - -
360B LYS* 6.5 1.3 - - - -
364B PHE* 5.5 0.4 - - - -
553B LEU* 6.0 1.6 - - - -
568B PHE* 3.6 0.9 - - - -
569B VAL 2.9 36.2 + - - +
570B ASN* 3.2 4.5 + - + +
571B GLY* 1.3 75.7 - - - +
573B TRP* 1.3 71.5 + - - +
574B VAL* 3.4 9.2 + - + +
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Residues in contact with TRP 573 (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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290B TYR* 5.5 1.6 - + - -
351B VAL* 6.1 0.6 - - - +
363B TYR* 3.3 45.5 - + + -
364B PHE* 4.8 21.8 - - + +
367B TYR* 6.3 0.7 - + - -
553B LEU* 3.1 50.5 - - + +
556B ILE* 3.8 15.5 - - + -
561B ILE* 3.4 35.7 - - + -
566B LYS* 3.4 29.0 - - + +
567B ILE 3.7 8.7 - - - -
568B PHE* 3.2 36.1 - + + -
571B GLY 3.7 1.4 + - - +
572B CYS* 1.3 79.4 - - - +
574B VAL* 1.3 58.5 + - - +
575B GLY 3.6 9.5 + - - -
576B ILE* 3.7 13.5 - - + -
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Residues in contact with VAL 574 (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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542B LEU* 3.6 23.8 - - + +
545B LEU* 4.6 3.1 - - + -
546B GLU* 6.1 2.2 - - + +
550B MET* 3.7 25.6 - - + -
551B GLU 3.7 7.6 - - - +
552B ASN* 4.3 3.5 - - - +
553B LEU* 3.4 17.4 + - - +
567B ILE* 3.1 14.1 + - + +
569B VAL* 3.6 38.4 - - + +
572B CYS* 3.7 12.8 - - - +
573B TRP* 1.3 73.7 - - - +
575B GLY* 1.3 58.3 + - - +
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Residues in contact with GLY 575 (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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550B MET* 4.5 3.8 - - - -
551B GLU 3.5 11.9 - - - -
553B LEU* 3.7 13.9 - - - +
556B ILE* 4.7 2.0 - - - -
567B ILE* 2.9 30.1 + - - +
573B TRP* 3.5 9.1 + - - -
574B VAL* 1.3 82.2 - - - +
576B ILE* 1.3 68.4 + - - +
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Residues in contact with ILE 576 (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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550B MET* 3.2 19.0 - - - +
551B GLU* 3.2 42.9 + - + +
556B ILE* 4.3 16.4 - - + -
560B ALA* 4.8 7.6 - - + +
561B ILE* 3.8 20.9 - - + -
564B ALA* 3.6 23.8 - - + +
565B THR 3.3 12.1 - - - +
566B LYS* 4.4 5.4 - - + -
567B ILE* 4.6 0.7 - - - +
573B TRP* 3.7 23.3 - - + -
575B GLY* 1.3 79.5 - - - +
577B HIS* 1.3 62.9 + - - +
578B LYS* 4.6 11.4 - - + -
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Residues in contact with HIS 577 (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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548B TRP* 3.5 27.1 + + - -
549B SER* 4.0 8.5 + - - -
550B MET* 3.7 30.1 - - + +
564B ALA* 4.0 0.7 - - - -
565B THR* 2.7 45.9 + - - +
567B ILE* 3.5 18.2 - - + -
576B ILE* 1.3 74.8 - - - +
578B LYS* 1.3 63.3 + - - +
579B ASP* 2.9 56.0 + - + -
582B GLN* 6.1 0.4 - - + -
583B LEU* 4.1 17.3 - - + +
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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