Contacts of the helix formed by residues 553 - 557 (chain B) in PDB entry 5FLZ
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 VAL 553 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500B LEU 3.7 6.3 - - - +
501B ALA* 3.9 11.9 - - - +
503B PRO* 4.1 5.6 - - - -
504B SER 4.6 0.7 - - - -
551B GLY* 3.4 6.4 + - - -
552B SER* 1.4 91.3 - - - +
554B GLY* 1.3 63.4 + - - +
555B TRP* 3.8 24.0 - - + +
556B ASP* 3.9 18.2 + - + +
557B VAL* 3.4 19.0 - - - +
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Residues in contact with GLY 554 (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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499B ILE 5.0 0.2 - - - -
500B LEU* 2.8 33.4 + - - +
502B THR 3.6 12.9 + - - -
503B PRO* 3.9 0.4 - - - +
504B SER* 4.0 19.9 - - - -
553B VAL* 1.3 72.6 - - - +
555B TRP* 1.4 61.1 + - - +
556B ASP 3.4 0.4 - - - -
557B VAL* 3.3 13.2 + - - +
558B PHE* 3.5 8.0 + - - +
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Residues in contact with TRP 555 (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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493B ILE* 3.9 17.9 - - + -
497B ASN* 3.3 45.3 - - - -
500B LEU* 3.4 43.8 + - + +
501B ALA* 3.5 18.4 - - - +
553B VAL* 3.3 22.4 - - + +
554B GLY* 1.4 74.2 - - - +
556B ASP* 1.3 62.8 + - - +
558B PHE* 3.3 12.0 + - - +
591B TRP* 3.1 37.6 - + + -
595B LYS* 3.2 36.8 - - + -
599B PHE* 3.4 27.3 - + - -
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Residues in contact with ASP 556 (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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546B LEU 5.3 0.3 - - - +
547B ASP* 3.0 37.6 - - - +
548B LEU 5.1 0.7 - - - +
551B GLY* 5.9 3.1 - - - +
553B VAL* 3.9 20.0 + - + +
554B GLY 3.4 0.2 - - - -
555B TRP* 1.3 77.8 - - - +
557B VAL* 1.3 64.5 + - + +
558B PHE 3.3 4.9 + - - +
588B ASN* 5.9 1.2 + - - -
591B TRP* 4.5 9.4 - - - -
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Residues in contact with VAL 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B SER* 3.4 27.8 - - - +
545B VAL* 3.7 22.9 - - + +
546B LEU 3.3 23.5 + - - +
547B ASP* 3.7 30.5 - - + +
549B GLY 4.5 4.5 - - - +
550B HIS* 4.9 1.1 - - - -
551B GLY 4.5 13.0 - - - +
553B VAL 3.4 20.6 - - - +
554B GLY 3.5 8.3 - - - +
555B TRP 3.3 0.2 - - - -
556B ASP* 1.3 77.8 - - + +
558B PHE* 1.4 61.7 + - - +
559B THR 3.7 0.9 + - - -
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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