Contacts of the strand formed by residues 554 - 560 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531C ALA* 4.9 15.0 - - - +
532C ALA 5.3 0.9 + - - -
545C VAL* 4.2 8.3 - - - -
552C VAL* 2.7 28.7 + - - +
553C PHE* 1.3 76.0 - - - +
555C ALA* 1.3 64.1 + - - +
556C THR* 5.4 1.9 + - - -
571C LYS* 5.5 2.1 - - - +
572C LEU 3.4 8.5 + - - -
573C GLN* 3.5 23.9 + - - +
614C PHE* 3.9 4.7 - - - -
626C TRP* 4.0 3.4 - - - -
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Residues in contact with ALA 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554C SER* 1.3 76.2 + - - +
556C THR* 1.3 62.9 + - - +
557C LEU* 4.0 10.6 - - + +
570C TYR 3.8 1.7 - - - +
571C LYS* 3.5 2.0 - - - +
572C LEU* 2.8 43.2 + - + +
614C PHE* 5.0 1.5 - - + -
618C TYR* 4.0 28.5 - - + -
626C TRP* 4.3 9.4 - - + -
640C PRO* 5.1 5.2 - - + -
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Residues in contact with THR 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554C SER* 5.4 1.4 + - - -
555C ALA* 1.3 74.0 - - - +
557C LEU* 1.3 68.5 + - - +
569C TYR* 5.5 4.9 - - + -
570C TYR 3.8 2.0 - - - +
571C LYS* 3.6 33.7 - - + +
640C PRO* 5.7 0.2 - - - +
641C LEU* 2.9 44.3 + - + +
643C ILE* 3.2 33.5 - - + +
695C LYS* 5.1 16.2 - - + -
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Residues in contact with LEU 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555C ALA* 4.1 17.9 - - + +
556C THR* 1.3 81.3 - - - +
558C GLY* 1.3 59.5 + - - +
569C TYR* 3.5 6.9 - - - +
570C TYR* 2.8 57.7 + - + +
572C LEU* 5.9 2.9 - - + -
618C TYR* 4.3 14.1 - - + -
621C LYS* 4.1 13.9 - - + -
622C THR* 4.2 10.5 - - - +
638C PHE* 3.7 30.5 - - + -
639C TYR 3.4 4.9 - - - +
640C PRO* 3.5 32.1 - - + -
641C LEU* 4.6 4.4 - - - +
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Residues in contact with GLY 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C LEU* 1.3 76.9 - - - +
559C LEU* 1.3 60.8 + - - +
568C SER 3.5 11.0 - - - -
569C TYR* 4.5 0.2 - - - -
633C LYS* 4.9 0.5 + - - -
638C PHE* 3.7 4.0 - - - -
639C TYR* 2.9 30.6 + - - +
641C LEU* 4.5 8.9 - - - +
738C THR* 3.3 22.2 - - - +
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Residues in contact with LEU 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A TRP 5.7 2.5 - - - +
558C GLY* 1.3 75.2 - - - +
560C VAL* 1.3 79.6 + - - +
561C ASP* 5.5 0.2 - - + -
566C THR* 4.3 5.9 - - - +
567C ASN* 3.5 1.8 + - - -
568C SER* 2.8 39.6 + - - +
633C LYS* 3.6 22.2 - - - +
636C LYS* 3.6 51.8 - - + +
637C LYS 4.2 4.3 - - - +
638C PHE* 3.7 34.3 - - + -
738C THR* 3.9 4.4 - - + +
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Residues in contact with VAL 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A TRP* 4.5 6.4 - - - +
559C LEU* 1.3 85.9 - - - +
561C ASP* 1.3 69.6 + - - +
562C ILE* 4.2 4.3 - - + +
566C THR* 3.3 12.6 - - - +
567C ASN* 4.1 11.7 - - + +
734C ASN* 3.3 29.0 - - - +
737C TYR* 3.8 11.0 - - + -
738C THR* 2.9 44.5 + - - +
749C PRO* 3.9 25.6 - - + -
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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