Contacts of the strand formed by residues 552 - 556 (chain A) in PDB entry 2R8O
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 LEU 552 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550A PRO* 3.4 1.5 - - - +
551A GLU* 1.3 81.1 - - - +
553A ILE* 1.3 66.7 + - - +
554A PHE* 3.9 15.5 - - + -
571A LEU* 3.6 31.4 - - + -
576A VAL* 4.2 14.4 - - + -
577A LYS 3.3 2.3 + - - +
578A ALA* 3.3 6.2 - - + -
579A ARG* 2.9 25.1 + - - +
605A VAL* 4.8 0.2 - - - -
607A ALA* 3.4 18.6 - - + +
609A VAL* 4.0 23.8 - - + -
659A ALA* 3.8 17.5 - - + +
662A LEU* 4.6 1.6 - - + -
663A LEU* 4.1 28.3 - - + -
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Residues in contact with ILE 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A PRO* 4.0 11.0 - - + -
552A LEU* 1.3 81.8 - - - +
554A PHE* 1.3 71.5 + - - +
555A ILE* 3.9 2.3 + - + +
579A ARG* 3.5 14.4 - - + +
581A VAL* 3.8 21.3 - - + -
600A VAL 4.3 4.5 - - - +
601A LEU* 4.1 15.7 - - + -
602A PRO* 3.8 30.3 - - + -
605A VAL* 3.7 29.4 - - + +
607A ALA 3.0 9.9 + - - +
608A ARG* 3.2 11.3 - - + +
609A VAL* 2.8 31.2 + - - +
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Residues in contact with PHE 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A LEU* 3.9 16.2 - - + -
553A ILE* 1.3 77.1 - - - +
555A ILE* 1.3 57.0 + - - +
556A ALA 4.1 0.4 - - - -
564A ALA* 4.2 28.3 - - + -
567A ALA* 3.8 8.5 - - + -
568A TYR* 3.9 22.0 - - + -
571A LEU* 3.5 27.6 - - + -
578A ALA* 4.8 3.8 - - + -
579A ARG 2.8 19.1 + - - +
580A VAL* 4.4 4.3 - - + -
581A VAL 2.8 31.2 + - - -
609A VAL* 3.2 32.8 - - + +
611A VAL* 4.3 5.2 - - + -
655A VAL* 3.5 26.9 - - + -
659A ALA* 3.9 12.1 - - + -
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Residues in contact with ILE 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ILE* 4.2 5.4 - - + +
554A PHE* 1.3 78.1 - - - +
556A ALA* 1.3 61.8 + - - +
581A VAL* 3.5 7.9 - - + +
583A MET* 4.0 25.6 - - + -
601A LEU* 3.6 33.0 - - + -
608A ARG* 4.4 13.0 - - + -
609A VAL 2.8 11.9 + - - +
610A ALA* 3.2 6.2 - - + +
611A VAL 2.8 26.3 + - - +
619A TRP* 3.9 26.2 - - + -
622A TYR* 3.9 30.7 - - + +
623A VAL* 4.5 7.0 - - + -
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Residues in contact with ALA 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A PHE 4.1 0.2 - - - -
555A ILE* 1.3 75.2 - - - +
557A THR* 1.3 65.3 + - - +
560A GLU 3.9 3.4 - - - +
561A VAL* 3.8 19.8 - - + +
564A ALA* 3.6 30.1 - - + -
580A VAL* 5.1 2.0 - - + -
581A VAL 3.0 8.9 + - - +
582A SER* 3.5 6.4 - - - -
583A MET* 2.9 24.9 + - - -
611A VAL* 3.4 14.4 - - + +
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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