Contacts of the strand formed by residues 485 - 490 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342B TRP* 3.1 7.1 + - - -
426B LEU* 3.9 3.4 - - - +
438B CYS 3.5 3.2 + - - -
439B ASN* 2.8 24.6 + - - -
440B ILE* 3.0 26.2 + - - +
468B SER 3.4 13.0 - - - -
480B PRO* 3.9 10.5 - - - -
481B ARG* 2.8 30.5 + - - -
483B HIS 3.6 3.9 + - - -
484B ALA* 1.3 76.0 - - - +
486B ILE* 1.3 67.5 + - - +
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Residues in contact with ILE 486 (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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422B PRO* 3.8 29.8 - - + +
423B GLN* 4.4 4.9 - - + +
426B LEU* 4.1 19.3 - - + -
440B ILE* 3.2 24.9 - - + +
442B VAL* 3.9 15.5 - - + -
457B VAL* 4.6 8.3 - - + -
461B ARG* 5.6 0.9 - - - -
468B SER 2.9 7.9 + - - +
469B CYS* 3.4 16.9 - - - -
470B GLY 2.9 24.8 + - - +
480B PRO* 3.8 4.3 - - - +
485B SER* 1.3 77.8 - - - +
487B MSE 1.3 62.7 + - - +
488B PHE* 3.3 30.4 - - + -
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Residues in contact with MSE 487 (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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342B TRP* 3.4 48.1 - - + +
440B ILE 2.8 10.5 + - - -
441B VAL* 3.2 23.8 - - + +
442B VAL 2.9 23.3 + - - -
470B GLY 3.5 12.8 - - - +
471B TYR* 4.1 2.9 - - - -
472B SER* 4.1 18.4 - - - -
479B LEU* 4.1 16.4 - - - -
480B PRO* 4.1 8.7 - - + -
486B ILE* 1.3 75.2 - - - +
488B PHE* 1.3 73.5 + - - +
489B CYS* 4.4 14.8 - - + -
493B VAL* 4.9 5.2 - - + -
494B LEU* 6.4 0.2 - - + -
497B LYS* 4.6 16.6 - - + -
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Residues in contact with PHE 488 (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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418B THR 4.7 1.8 - - - -
422B PRO* 4.5 13.7 - - + -
442B VAL* 3.1 34.3 - - + +
444B GLN* 4.3 7.6 - - + -
450B ALA* 3.7 21.5 - - - +
453B VAL* 3.4 26.5 - - + -
454B ALA* 4.0 18.8 - - + -
457B VAL* 3.9 29.6 - - + -
469B CYS* 4.5 6.3 - - - -
470B GLY 3.0 18.3 + - - +
471B TYR* 3.1 24.3 - - - +
472B SER 3.1 4.5 + - - -
486B ILE* 3.3 28.7 - - + -
487B MSE 1.3 76.1 - - - +
489B CYS* 1.3 60.9 + - - +
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Residues in contact with CYS 489 (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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441B VAL* 3.6 29.2 - - - -
442B VAL 2.9 7.7 + - - -
443B THR* 3.1 9.8 - - - -
444B GLN* 2.9 25.1 + - - -
450B ALA* 3.9 11.0 - - - +
472B SER* 3.1 22.9 - - - +
487B MSE 4.4 4.7 - - + -
488B PHE* 1.3 74.9 - - - +
490B THR* 1.3 73.0 + - - +
493B VAL* 3.9 12.8 - - + -
494B LEU* 3.8 17.7 - - - -
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Residues in contact with THR 490 (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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443B THR* 4.8 0.7 - - - -
444B GLN 3.8 7.4 - - - +
445B PRO 5.5 0.4 - - - -
446B ARG* 3.9 10.1 - - - +
447B ARG* 3.8 33.2 - - + +
450B ALA* 4.1 0.9 - - + +
472B SER 3.8 1.4 + - - -
473B VAL* 4.1 16.4 - - + -
474B ARG* 4.6 2.9 + - - +
489B CYS* 1.3 84.5 - - - +
491B VAL* 1.3 66.3 + - - +
492B GLY* 4.2 4.3 + - - -
493B VAL* 3.4 22.3 + - - +
494B LEU 3.3 14.7 + - - -
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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