Contacts of the strand formed by residues 482 - 487 (chain A) in PDB entry 2LLL
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 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480A ASN* 3.3 22.6 + - - +
481A TRP* 1.3 74.3 - - - +
483A ILE* 1.3 63.1 + - - +
484A LYS* 3.9 24.0 - - - +
494A ALA* 4.5 14.8 - - + -
495A TYR 3.1 14.6 - - - +
496A LYS* 3.9 13.7 - - + -
497A PHE* 4.2 1.3 - - - -
544A LEU* 4.8 0.4 - - - -
545A VAL* 3.0 55.2 + - + +
546A ASN 4.4 0.8 + - - -
547A ALA 5.2 2.0 + - - -
549A GLY* 3.5 30.1 + - - +
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Residues in contact with ILE 483 (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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456A ILE* 5.6 1.3 - - + -
466A VAL* 3.9 26.2 - - + -
468A LEU* 3.8 12.6 - - + -
482A ARG* 1.3 70.3 - - - +
484A LYS* 1.3 58.4 + - - +
485A ARG 3.4 5.4 + - - -
493A ILE 3.4 1.2 - - - +
494A ALA* 3.2 2.1 - - - -
495A TYR* 3.0 30.6 + - + +
497A PHE* 3.6 34.1 - - + -
511A VAL* 4.5 6.3 - - + -
534A TRP* 3.6 26.5 - - + -
542A THR* 3.6 28.0 - - + -
543A VAL 3.1 13.2 - - - +
544A LEU* 3.9 12.1 - - + -
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Residues in contact with LYS 484 (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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482A ARG* 3.8 25.1 + - + +
483A ILE* 1.3 68.4 - - - +
485A ARG* 1.3 60.1 + - - +
486A GLN* 3.5 14.7 + - + +
493A ILE 3.3 9.0 - - - +
494A ALA* 3.8 17.0 - - + +
541A ARG 3.0 6.8 - - - +
542A THR* 4.5 0.2 - - - -
543A VAL* 2.8 44.4 + - + +
545A VAL* 3.7 24.2 - - + +
549A GLY 5.4 0.2 + - - -
551A GLU* 3.0 26.1 + - + +
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Residues in contact with ARG 485 (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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459A ILE* 3.2 21.2 - - - +
463A GLY* 2.9 34.2 + - - -
465A PHE 2.9 24.5 + - - -
466A VAL* 3.2 20.7 - - - +
483A ILE 3.4 2.8 + - - -
484A LYS* 1.3 68.7 - - - +
486A GLN* 1.3 57.7 + - - +
487A VAL* 3.9 2.9 + - + +
491A GLU 4.0 1.6 - - - +
492A GLU* 3.6 2.9 - - - -
493A ILE* 2.9 32.8 + - + +
534A TRP* 2.9 57.1 + - + +
535A GLY* 3.2 21.0 - - - +
540A PHE* 3.6 19.6 - - + -
541A ARG 3.5 3.6 - - - -
542A THR* 3.0 26.9 + - + +
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Residues in contact with GLN 486 (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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484A LYS* 4.2 17.3 - - + +
485A ARG* 1.3 70.7 - - - +
487A VAL* 1.3 63.7 + - - +
488A LEU 4.1 0.5 + - - -
492A GLU* 3.6 30.0 + - + +
540A PHE* 3.5 0.9 - - - -
541A ARG* 2.9 86.5 + - + +
543A VAL* 4.0 16.6 - - - +
554A MET* 5.8 0.7 - - - -
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Residues in contact with VAL 487 (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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485A ARG* 4.5 2.2 - - + +
486A GLN* 1.3 75.0 - - - +
488A LEU* 1.3 61.4 + - - +
489A GLU* 3.1 20.4 - - + +
490A GLY* 3.1 19.8 + - - -
491A GLU* 3.0 27.4 + - + +
492A GLU* 5.0 2.8 - - - +
535A GLY* 3.4 32.5 - - - +
536A THR 3.5 21.5 - - - +
537A GLY* 3.7 11.0 - - - -
539A SER 3.4 14.6 - - - +
540A PHE* 3.7 14.1 - - + -
541A ARG* 5.7 1.1 - - - -
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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