Contacts of the strand formed by residues 485 - 490 (chain A) in PDB entry 3LLM
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 SER 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A TRP* 3.1 17.6 + - - -
426A LEU* 3.8 4.1 - - - +
438A CYS 3.5 3.9 + - - +
439A ASN* 3.2 9.9 + - - +
440A ILE* 2.9 25.6 + - - +
468A SER 3.3 16.4 - - - -
480A PRO* 3.9 10.5 - - - -
481A ARG* 2.6 32.7 + - - -
483A HIS 3.6 2.7 + - - -
484A ALA* 1.3 76.9 - - - +
486A ILE* 1.3 66.1 + - - +
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Residues in contact with ILE 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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422A PRO* 3.8 28.9 - - + +
423A GLN* 4.4 4.0 - - + +
426A LEU* 4.2 19.5 - - + -
440A ILE* 3.1 27.6 - - + +
442A VAL* 3.7 20.0 - - + -
457A VAL* 4.6 9.0 - - + -
461A ARG* 5.5 0.2 - - - -
468A SER 2.9 9.0 + - - +
469A CYS* 3.3 19.8 - - - +
470A GLY 3.0 24.6 + - - +
480A PRO* 3.8 5.2 - - - +
485A SER* 1.3 77.7 - - - +
487A MSE 1.3 61.0 + - - +
488A PHE* 3.7 24.2 - - + -
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Residues in contact with MSE 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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342A TRP* 3.6 48.7 - - + +
440A ILE 2.8 8.5 + - - -
441A VAL* 3.2 23.0 - - + +
442A VAL 2.8 29.2 + - - -
470A GLY 3.7 4.3 - - - +
471A TYR* 4.2 11.7 - - - +
472A SER* 3.8 24.0 - - - -
479A LEU* 4.0 18.2 - - - -
480A PRO* 4.4 5.6 - - + -
486A ILE* 1.3 75.2 - - - +
488A PHE* 1.3 68.4 + - - +
489A CYS* 4.7 8.5 - - + -
493A VAL* 5.1 5.2 - - + -
494A LEU* 6.0 0.4 - - + -
497A LYS* 4.7 18.6 - - + +
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Residues in contact with PHE 488 (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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418A THR 4.8 2.5 - - - -
422A PRO* 4.6 11.9 - - + -
442A VAL* 3.2 34.8 - - + +
444A GLN* 4.5 7.9 - - + -
450A ALA* 3.5 24.5 - - - +
453A VAL* 3.3 32.8 - - + -
454A ALA* 3.7 18.2 - - + -
457A VAL* 3.9 21.1 - - + -
469A CYS* 4.6 5.6 - - - -
470A GLY 3.1 19.1 + - - +
471A TYR* 3.1 22.3 - - - +
472A SER 3.2 4.9 + - - -
486A ILE* 3.7 25.4 - - + -
487A MSE 1.3 75.7 - - - +
489A CYS* 1.3 61.8 + - - +
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Residues in contact with CYS 489 (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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441A VAL* 3.8 26.5 - - - -
442A VAL 2.9 9.6 + - - -
443A THR* 3.2 8.3 - - - -
444A GLN* 2.8 26.9 + - - +
450A ALA* 4.0 11.1 - - - +
472A SER* 3.2 20.2 - - - +
487A MSE 4.7 5.2 - - + -
488A PHE* 1.3 76.3 - - - +
490A THR* 1.3 72.8 + - - +
493A VAL* 4.0 12.3 - - + -
494A LEU* 4.2 17.7 - - - -
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Residues in contact with THR 490 (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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443A THR* 4.6 0.9 - - - -
444A GLN 3.9 6.5 - - - +
445A PRO 5.4 0.7 - - - -
446A ARG* 4.0 5.6 - - - +
447A ARG* 3.6 41.7 - - + +
450A ALA* 4.9 0.4 - - + -
472A SER 3.9 2.3 + - - -
473A VAL* 4.4 9.1 - - + -
474A ARG 4.6 2.1 + - - +
489A CYS* 1.3 84.4 - - - +
491A VAL* 1.3 66.6 + - - +
492A GLY* 4.1 4.9 - - - -
493A VAL* 3.1 36.0 + - - +
494A LEU 3.3 7.6 + - - -
496A ARG* 5.2 1.9 + - - -
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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