Contacts of the strand formed by residues 518 - 524 (chain I) in PDB entry 3BTQ
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 ILE 518 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E TYR* 3.8 4.9 - - - +
41E PHE* 4.1 20.4 - - + -
57E HIS 4.3 8.7 - - - +
58E CYS* 5.4 0.7 - - - -
59E TYR 5.7 3.4 - - - +
60E LYS* 3.9 24.5 - - + +
516I ALA* 3.9 23.6 - - + -
517I ARG* 1.3 77.6 - - - +
519I ILE* 1.3 64.4 + - - +
520I ARG* 3.5 35.1 + - + +
534I VAL* 3.6 2.9 - - - +
535I TYR* 2.8 45.4 + - + +
537I GLY* 3.9 19.1 - - - -
602I SO4 5.6 0.7 - - - +
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Residues in contact with ILE 519 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E TYR* 3.0 51.6 + - + +
60E LYS* 5.6 0.7 + - - -
517I ARG* 4.5 16.4 - - - +
518I ILE* 1.3 73.9 - - - +
520I ARG* 1.3 68.5 + - - +
521I TYR* 5.3 5.5 - - + -
532I THR* 3.8 33.7 - - + -
533I PHE 3.6 6.7 - - - +
534I VAL* 5.1 4.9 - - + -
546I LYS 5.3 3.5 - - - +
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Residues in contact with ARG 520 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E LYS* 5.0 6.1 - - - +
603E SO4 4.8 5.1 + - - -
518I ILE* 3.5 20.2 + - + +
519I ILE* 1.3 78.1 + - - +
521I TYR* 1.3 68.7 + - - +
532I THR* 3.1 8.1 - - - -
533I PHE* 3.0 46.2 + - + -
535I TYR* 3.7 31.0 - - + -
544I ASN* 2.9 30.9 + - - +
545I PHE 3.3 19.9 - - - +
546I LYS* 3.9 36.9 - - - +
602I SO4 3.4 35.6 + - - -
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Residues in contact with TYR 521 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519I ILE* 5.3 5.3 - - + +
520I ARG* 1.3 76.7 - - - +
522I PHE* 1.3 61.4 + - - +
530I CYS* 4.4 10.1 - - + -
531I GLN* 3.1 16.6 - - - -
532I THR* 3.6 24.7 - - + +
533I PHE* 3.7 2.4 - - - -
544I ASN* 3.3 6.9 - - - -
545I PHE* 2.7 41.2 + - + +
546I LYS 4.1 6.1 - - - -
547I SER* 3.6 30.5 - - - +
548I ALA* 3.7 36.4 - - + +
551I CYS* 4.2 11.2 - - + -
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Residues in contact with PHE 522 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507I GLU 4.9 0.9 - - - -
508I PRO* 5.6 0.2 - - + -
509I PRO* 3.7 37.2 - - + -
521I TYR* 1.3 74.1 - - - +
523I TYR* 1.3 71.5 + - - +
524I ASN* 3.8 30.7 - - + -
530I CYS* 3.2 1.6 - - - -
531I GLN* 2.8 71.0 + - + -
532I THR 3.7 11.9 - - - -
533I PHE* 3.4 22.7 - + + -
543I ASN* 3.5 29.8 - - - +
551I CYS* 3.7 6.1 - - - -
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Residues in contact with TYR 523 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505I CYS* 3.4 28.3 - - + +
506I LEU 5.6 0.3 - - - -
507I GLU 4.6 1.2 - - - +
522I PHE* 1.3 76.7 - - - +
524I ASN* 1.3 60.6 + - - +
525I ALA* 3.5 27.1 + - + -
528I GLY* 3.9 16.3 - - - -
529I LEU* 3.9 18.4 - - - -
530I CYS* 3.9 15.3 - - - -
543I ASN* 2.8 29.8 + - - +
551I CYS* 3.6 8.0 - - - -
552I LEU* 5.2 2.0 - - + -
555I CYS* 3.5 44.0 - - + -
556I GLY* 4.0 10.1 - - - -
557I GLY* 3.6 7.0 + - - -
558I ALA* 3.2 36.4 + - + -
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Residues in contact with ASN 524 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522I PHE* 3.5 23.7 + - + -
523I TYR* 1.3 71.6 - - - +
525I ALA* 1.3 53.0 + - - +
526I LYS* 3.1 22.4 + - - +
527I ALA* 3.2 16.2 + - + +
528I GLY* 2.7 31.4 + - - -
529I LEU 2.8 21.8 + - - +
531I GLN* 3.0 30.4 + - + -
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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
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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