Contacts of the strand formed by residues 578 - 584 (chain A) in PDB entry 3BRF
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 ARG 578 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569A GLU 3.9 0.7 - - - +
570A VAL* 4.0 3.7 - - - +
571A ASP* 3.0 43.1 + - - +
576A ALA 3.5 9.3 + - - +
577A SER* 1.3 76.2 - - - +
579A VAL* 1.3 61.7 + - - +
580A GLU* 4.2 4.6 + - + +
602A THR* 6.3 0.4 - - - -
610A HIS* 3.3 43.8 + - + +
611A CYS* 3.4 18.8 - - - +
612A SER* 4.8 10.3 + - - +
613A ILE* 5.7 0.2 - - - -
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Residues in contact with VAL 579 (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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568A LEU* 4.3 22.7 - - + -
569A GLU 3.5 11.9 - - - +
570A VAL* 4.7 11.4 - - + +
578A ARG* 1.3 73.4 - - - +
580A GLU* 1.3 71.9 + - - +
581A LEU* 4.2 7.9 - - + +
594A PHE* 3.6 31.6 - - + -
609A LEU 4.2 0.5 - - - +
611A CYS* 2.8 52.4 + - - +
612A SER 4.2 3.4 - - - +
613A ILE* 4.3 11.4 - - + -
640A ILE* 5.8 0.2 - - + -
656A PHE* 5.7 4.9 - - + -
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Residues in contact with GLU 580 (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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567A SER 3.9 0.2 - - - +
568A LEU* 3.6 7.8 - - - +
569A GLU* 3.0 45.7 + - + +
571A ASP* 5.2 10.3 - - - +
578A ARG* 5.3 4.2 + - + +
579A VAL* 1.3 76.5 - - - +
581A LEU* 1.3 67.9 + - - +
582A HIS* 4.1 18.7 + - - +
604A ARG* 4.0 26.3 + - - -
608A SER* 5.3 2.1 - - - -
609A LEU 3.6 5.6 + - - +
610A HIS* 3.5 31.3 + - + +
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Residues in contact with LEU 581 (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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565A VAL* 4.0 29.4 - - + -
567A SER 3.8 2.9 - - - -
568A LEU* 3.8 20.4 - - + -
579A VAL* 4.2 14.1 - - + +
580A GLU* 1.3 82.6 - - - +
582A HIS* 1.3 64.9 + - - +
586A PHE* 3.6 5.8 - - + -
592A VAL* 5.0 7.6 - - + -
594A PHE* 6.3 0.7 - - + -
608A SER* 3.5 5.2 - - - -
609A LEU* 2.9 54.7 + - + +
611A CYS* 4.8 8.5 - - - -
640A ILE* 4.6 17.3 - - + -
642A LEU* 4.3 22.0 - - + -
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Residues in contact with HIS 582 (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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565A VAL* 3.3 5.4 - - - +
566A GLY* 2.4 33.7 + - - -
567A SER* 3.5 25.2 + - - +
569A GLU* 3.2 40.1 + - + +
580A GLU* 4.1 22.7 + - - +
581A LEU* 1.3 81.9 + - - +
583A GLY* 1.3 51.2 + - - +
586A PHE* 3.7 3.6 - - - -
604A ARG* 5.0 5.6 - - - -
607A GLU 3.6 13.8 + - - +
608A SER* 4.5 8.5 - - - -
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Residues in contact with GLY 583 (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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564A VAL* 3.0 12.8 - - - -
566A GLY* 3.9 5.2 - - - -
582A HIS* 1.3 76.6 - - - +
584A ARG* 1.3 67.9 + - - +
586A PHE* 3.5 4.7 - - - -
606A GLU 4.2 0.7 - - - -
607A GLU* 3.1 34.5 + - - +
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Residues in contact with ARG 584 (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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359A VAL* 3.7 22.1 - - - +
360A SER 4.5 6.7 + - - -
361A GLN* 4.7 13.9 + - - +
546A TYR* 3.0 31.3 + - - -
562A CYS 5.5 0.4 + - - -
563A PRO* 3.4 1.2 - - - +
564A VAL* 2.9 57.5 + - + +
583A GLY* 1.3 78.9 - - - +
585A ASP* 1.3 82.6 + - - +
586A PHE* 3.3 5.3 + - - -
606A GLU 3.5 2.5 - - - -
607A GLU* 4.4 5.8 - - - +
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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