Contacts of the strand formed by residues 479 - 488 (chain B) in PDB entry 3LMK
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 PHE 479 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B TYR* 5.2 3.8 - - - -
318B GLN* 3.4 35.8 + - + +
319B ARG* 4.3 21.1 - - + -
322B VAL* 3.9 26.7 - - + -
471B PHE* 3.7 22.6 - + + -
472B LYS 3.3 9.0 - - - +
473B GLU* 3.7 46.9 - - + -
474B MET* 4.4 1.1 - - - +
477B ASP* 3.9 24.0 - - - -
478B TYR* 1.3 88.3 - - - +
480B ASP* 1.3 67.0 + - - +
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Residues in contact with ASP 480 (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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311B TYR* 2.6 35.8 + - - -
470B ASN 3.6 0.5 - - - +
471B PHE* 3.8 11.1 - - - -
472B LYS 3.0 31.3 + - - +
474B MET* 4.2 11.3 - - + +
478B TYR* 3.1 27.4 + - + +
479B PHE* 1.3 77.1 - - - +
481B TYR* 1.3 85.0 + - - +
482B ILE* 3.7 9.6 + - + +
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Residues in contact with TYR 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B TRP* 2.9 27.1 + + - -
308B ALA 3.4 22.0 - - - -
309B ASP* 3.6 38.4 - - + -
310B ARG 2.9 11.2 + - - -
311B TYR* 3.9 23.8 - + - +
314B THR* 2.8 23.4 + - - +
326B THR* 4.6 2.7 - - + -
469B MET* 4.4 19.7 - - + +
470B ASN 3.6 2.0 - - - -
471B PHE* 3.4 36.3 - + + -
480B ASP* 1.3 87.7 + - - +
482B ILE* 1.3 66.8 + - - +
483B ASN 4.3 0.5 + - - -
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Residues in contact with ILE 482 (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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469B MET* 3.4 3.6 - - - -
470B ASN* 2.8 42.6 + - + +
472B LYS* 4.2 14.6 - - + -
474B MET* 3.7 42.6 - - + -
480B ASP* 3.8 11.7 - - + +
481B TYR* 1.3 82.7 - - - +
483B ASN* 1.3 75.1 + - - +
484B VAL* 3.3 13.2 + - + +
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Residues in contact with ASN 483 (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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467B GLU* 3.6 14.9 - - - +
469B MET* 3.3 32.5 - - + +
481B TYR 4.3 0.4 + - - -
482B ILE* 1.3 79.1 - - - +
484B VAL* 1.3 64.5 + - - +
485B GLY* 3.5 21.6 + - - +
495B ASP* 3.7 13.9 + - - +
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Residues in contact with VAL 484 (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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468B ILE* 2.9 12.7 + - + +
469B MET 5.0 0.4 - - - -
470B ASN* 3.7 25.4 - - + +
472B LYS* 5.8 4.5 - - - -
482B ILE* 3.3 20.4 + - + +
483B ASN* 1.3 78.4 - - - +
485B GLY* 1.3 59.4 + - - +
494B MET* 3.7 22.9 - - + -
495B ASP* 2.8 43.2 + - + +
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Residues in contact with GLY 485 (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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467B GLU* 3.7 1.2 - - - -
468B ILE* 2.9 27.1 + - - +
483B ASN* 3.5 16.3 + - - +
484B VAL* 1.3 80.5 - - - +
486B SER* 1.3 63.7 + - - -
493B LYS 3.2 13.0 - - - -
494B MET* 4.1 10.3 - - - -
495B ASP* 4.3 5.2 - - - -
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Residues in contact with SER 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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466B TYR 3.2 13.9 - - - -
467B GLU* 4.7 2.9 - - - -
468B ILE* 3.3 7.4 - - - +
485B GLY* 1.3 75.6 - - - -
487B TRP* 1.3 62.1 + - - +
488B ASP* 5.1 3.2 + - - +
491B GLU 5.2 0.3 + - - -
492B LEU* 3.5 7.8 - - - +
493B LYS* 2.8 45.4 + - - +
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Residues in contact with TRP 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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197B GLN* 3.7 43.3 - - + -
200B ARG* 3.4 27.1 - - + -
201B ALA* 3.5 27.4 - - + +
204B ASP* 2.9 19.9 + - - -
465B ARG* 3.4 2.6 - - - +
466B TYR* 2.9 52.8 + + + +
468B ILE* 4.2 5.4 - - + -
486B SER* 1.3 75.3 - - - +
488B ASP* 1.3 67.9 + - - +
489B ASN* 3.8 7.9 - - - -
490B GLY* 3.3 38.2 + - - -
491B GLU 3.4 3.8 - - - -
492B LEU* 3.6 35.0 - - + +
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Residues in contact with ASP 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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464B GLY 3.8 5.0 - - - +
465B ARG* 3.4 41.9 + - + +
486B SER* 5.4 4.3 - - - +
487B TRP* 1.3 79.5 - - - +
489B ASN* 1.3 80.0 + - - +
490B GLY 3.1 1.6 - - - -
491B GLU* 3.0 27.1 + - + +
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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