Contacts of the strand formed by residues 554 - 560 (chain F) in PDB entry 4OQB
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 SER 554 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531F ALA* 4.9 15.0 - - - +
532F ALA 5.3 0.7 + - - -
545F VAL* 4.2 7.9 - - - -
552F VAL* 2.7 29.3 + - - +
553F PHE* 1.3 76.5 - - - +
555F ALA* 1.3 63.1 + - - +
556F THR* 5.4 2.4 + - - -
571F LYS* 5.4 2.1 - - - +
572F LEU 3.4 7.9 - - - -
573F GLN* 3.5 24.6 + - - +
614F PHE* 3.9 4.4 - - - -
626F TRP* 4.4 2.5 - - - -
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Residues in contact with ALA 555 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554F SER* 1.3 75.6 + - - +
556F THR* 1.3 64.3 + - - +
557F LEU* 4.0 10.9 - - + +
570F TYR 3.8 1.4 - - - +
571F LYS* 3.5 1.7 - - - +
572F LEU* 2.8 42.4 + - + +
614F PHE* 4.9 1.3 - - + -
618F TYR* 4.0 28.5 - - + -
626F TRP* 4.3 10.1 - - + -
640F PRO* 5.2 4.7 - - + -
641F LEU 5.7 0.4 - - - -
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Residues in contact with THR 556 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554F SER* 5.4 1.7 + - - -
555F ALA* 1.3 73.2 - - - +
557F LEU* 1.3 69.6 + - - +
569F TYR* 5.5 4.7 - - + -
570F TYR 3.8 2.5 - - - +
571F LYS* 3.6 34.6 - - + +
641F LEU* 2.9 43.4 + - + +
643F ILE* 3.2 32.3 - - + +
695F LYS* 5.0 17.5 - - + -
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Residues in contact with LEU 557 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555F ALA* 4.1 18.2 - - + +
556F THR* 1.3 80.7 - - - +
558F GLY* 1.3 60.3 + - - +
569F TYR* 3.5 6.9 - - - +
570F TYR* 2.8 58.6 + - + +
572F LEU* 5.8 2.5 - - + +
618F TYR* 4.3 14.4 - - + +
621F LYS* 4.1 13.9 - - + -
622F THR* 4.2 11.4 - - - +
638F PHE* 3.7 30.7 - - + -
639F TYR 3.4 5.2 - - - +
640F PRO* 3.5 31.4 - - + -
641F LEU* 4.6 4.4 - - - +
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Residues in contact with GLY 558 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557F LEU* 1.3 76.8 - - - +
559F LEU* 1.3 62.1 + - - +
568F SER 3.5 11.0 - - - -
633F LYS* 4.9 0.3 + - - -
638F PHE* 3.7 4.2 - - - -
639F TYR* 2.9 31.8 + - - +
641F LEU* 4.5 8.4 - - - +
738F THR* 3.3 21.6 - - - +
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Residues in contact with LEU 559 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D TRP 5.7 2.9 - - - +
558F GLY* 1.3 75.9 - - - +
560F VAL* 1.3 78.8 + - - +
561F ASP* 5.5 0.2 - - + -
566F THR* 4.2 6.7 - - + +
567F ASN* 3.5 1.3 + - - -
568F SER* 2.8 39.4 + - - +
633F LYS* 3.6 22.0 - - - +
636F LYS* 3.6 52.9 - - + +
637F LYS 4.1 4.0 - - - +
638F PHE* 3.7 34.9 - - + -
738F THR* 3.9 5.0 - - + +
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Residues in contact with VAL 560 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D TRP 4.7 5.7 - - - +
559F LEU* 1.3 85.4 - - - +
561F ASP* 1.3 69.6 + - - +
562F ILE* 4.2 4.0 - - + +
566F THR 3.3 13.9 - - - +
567F ASN* 4.1 11.9 - - + +
734F ASN* 3.2 28.0 - - - +
737F TYR* 3.8 11.2 - - + -
738F THR* 2.9 45.1 + - - +
749F PRO* 3.9 24.9 - - + -
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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