Contacts of the strand formed by residues 552 - 556 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550B PRO* 3.3 2.8 + - - +
551B GLU* 1.3 81.7 - - + +
553B ILE* 1.3 66.3 + - - +
554B PHE* 3.8 15.5 - - + -
571B LEU* 3.7 29.8 - - + -
576B VAL* 4.5 6.5 - - + -
577B LYS 3.3 5.5 + - - +
578B ALA* 3.3 7.4 - - + -
579B ARG 3.0 24.3 + - - +
605B VAL* 4.8 0.2 - - - -
607B ALA* 3.4 15.0 - - + +
609B VAL* 3.8 24.5 - - + -
659B ALA* 3.8 15.0 - - + +
662B LEU* 4.3 7.4 - - + -
663B LEU* 4.2 30.5 - - + -
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Residues in contact with ILE 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B PRO* 4.1 6.3 - - + -
552B LEU* 1.3 80.4 - - - +
554B PHE* 1.3 74.9 + - - +
555B ILE* 3.9 2.8 + - + +
579B ARG* 3.5 23.6 - - - +
581B VAL* 3.9 20.4 - - + -
600B VAL 4.3 2.2 - - - +
601B LEU* 4.2 15.5 - - + -
602B PRO* 3.8 30.3 - - + -
605B VAL* 3.6 29.8 - - + +
607B ALA 3.0 9.1 + - - +
608B ARG* 3.3 11.8 - - + +
609B VAL* 2.8 26.3 + - - +
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Residues in contact with PHE 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B LEU* 3.8 20.6 - - + -
553B ILE* 1.3 77.5 - - - +
555B ILE* 1.3 56.3 + - - +
556B ALA 4.1 0.4 - - - -
564B ALA* 4.1 29.4 - - + -
567B ALA* 3.9 9.2 - - + -
568B TYR* 3.9 21.5 - - + -
571B LEU* 3.5 28.0 - - + -
578B ALA* 4.7 4.7 - - + -
579B ARG 2.8 17.7 + - - +
580B VAL* 3.5 4.7 - - + -
581B VAL 2.8 31.4 + - - -
609B VAL* 3.2 32.3 - - + +
611B VAL* 4.3 5.6 - - + -
655B VAL* 3.6 26.0 - - + -
659B ALA* 3.9 8.5 - - + -
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Residues in contact with ILE 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B ILE* 4.2 7.0 - - + +
554B PHE* 1.3 75.6 - - - +
556B ALA* 1.3 62.6 + - - +
581B VAL* 3.5 8.3 - - + +
583B MET* 4.1 26.9 - - + -
601B LEU* 3.7 30.3 - - + -
608B ARG* 4.5 7.9 - - + -
609B VAL 2.8 12.3 + - - +
610B ALA* 3.2 6.8 - - - +
611B VAL 2.8 25.8 + - - +
619B TRP* 3.8 25.7 - - + -
622B TYR* 3.9 33.2 - - + +
623B VAL* 4.4 9.9 - - + -
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Residues in contact with ALA 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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555B ILE* 1.3 75.8 - - - +
557B THR* 1.3 67.8 + - - +
560B GLU 3.9 2.9 - - - +
561B VAL* 3.7 19.6 - - + +
564B ALA* 3.6 29.2 - - + -
580B VAL* 5.2 1.3 - - + -
581B VAL 3.0 9.2 + - - +
582B SER* 3.5 6.4 - - - -
583B MET 2.9 24.6 + - - -
611B VAL* 3.4 14.8 - - + +
619B TRP* 5.9 0.2 - - - -
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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