Contacts of the strand formed by residues 479 - 488 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A TYR* 5.2 4.3 - - - -
318A GLN* 3.4 36.8 + - + +
319A ARG* 3.3 41.1 - - + -
322A VAL* 4.0 22.9 - - + -
471A PHE* 3.7 23.1 - + + -
472A LYS 3.3 7.4 - - - +
473A GLU* 3.6 34.1 - - + -
474A MET 4.4 0.2 - - - +
477A ASP* 3.7 24.9 - - - -
478A TYR* 1.3 85.5 - - - +
480A ASP* 1.3 64.8 + - - +
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Residues in contact with ASP 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A TYR* 2.5 35.9 + - - -
470A ASN 3.4 1.2 - - - +
471A PHE* 4.1 9.3 - - - -
472A LYS 3.0 30.4 + - - +
474A MET* 4.5 10.2 - - + +
478A TYR* 4.1 23.5 + - + -
479A PHE* 1.3 75.8 - - - +
481A TYR* 1.3 86.4 + - - +
482A ILE* 3.6 10.2 + - + +
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Residues in contact with TYR 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A TRP* 3.0 23.3 + + - -
308A ALA 3.5 21.5 - - - -
309A ASP* 3.7 38.6 - - + -
310A ARG 2.9 15.8 + - - -
311A TYR* 3.8 24.0 - + - +
314A THR* 2.9 23.8 + - - +
326A THR* 4.6 2.2 - - + -
469A MET* 4.4 19.7 - - + +
470A ASN 3.3 5.2 - - - +
471A PHE* 3.5 39.7 - + + -
480A ASP* 1.3 85.9 + - - +
482A ILE* 1.3 64.9 + - - +
483A ASN 4.1 1.2 + - - -
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Residues in contact with ILE 482 (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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469A MET* 3.4 2.8 - - - -
470A ASN 2.7 37.6 + - - +
472A LYS* 3.7 34.3 - - + -
474A MET* 3.7 28.0 - - + -
480A ASP* 3.9 10.3 - - + +
481A TYR* 1.3 81.2 - - - +
483A ASN* 1.3 66.1 + - - +
484A VAL* 3.0 25.4 + - + +
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Residues in contact with ASN 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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467A GLU* 3.4 24.8 - - - +
469A MET* 3.1 33.1 - - + +
481A TYR 4.1 2.0 + - - -
482A ILE* 1.3 74.4 - - - +
484A VAL* 1.3 58.6 + - - +
485A GLY* 3.7 16.6 + - - +
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Residues in contact with VAL 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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209A TYR* 4.7 5.4 - - - +
468A ILE* 2.8 16.9 + - + +
469A MET 4.9 0.4 - - - -
470A ASN* 3.4 30.5 - - + +
472A LYS* 5.8 0.7 - - + -
482A ILE* 3.0 27.0 + - + +
483A ASN* 1.3 74.4 - - - +
485A GLY* 1.3 54.8 + - - +
494A MET* 3.7 26.1 - - + -
495A ASP* 3.8 24.1 + - - +
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Residues in contact with GLY 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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467A GLU* 3.6 4.7 - - - +
468A ILE* 3.0 30.2 + - - +
483A ASN* 3.6 14.2 + - - +
484A VAL* 1.3 80.6 - - - +
486A SER* 1.3 64.1 + - - -
493A LYS 3.1 14.1 - - - -
494A MET* 4.3 2.5 - - - -
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Residues in contact with SER 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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330A GLN* 5.3 8.3 - - - -
466A TYR 3.3 12.1 - - - -
467A GLU* 4.7 2.9 - - - -
468A ILE* 3.5 9.5 - - - +
483A ASN* 6.0 0.4 - - - -
485A GLY* 1.3 75.3 - - - -
487A TRP* 1.3 62.4 + - - +
488A ASP* 6.1 1.5 - - - +
491A GLU 3.9 1.1 - - - +
492A LEU* 3.7 0.7 - - - -
493A LYS* 2.9 50.1 + - - +
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Residues in contact with TRP 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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197A GLN* 3.7 40.4 - - + -
200A ARG* 3.9 24.0 - - + -
201A ALA* 3.4 32.6 - - + +
204A ASP* 3.3 19.0 + - - -
465A ARG* 3.4 6.5 - - - +
466A TYR* 2.9 52.8 + + + +
468A ILE* 3.8 10.1 - - + +
486A SER* 1.3 74.9 - - - +
488A ASP* 1.3 64.1 + - - +
489A ASN* 3.7 9.4 - - - -
490A GLY* 3.2 39.7 + - - -
491A GLU 3.3 3.8 - - - -
492A LEU* 3.5 31.6 - - + -
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Residues in contact with ASP 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A GLY 4.1 4.9 - - - +
465A ARG* 2.8 40.9 + - + +
486A SER* 6.1 2.0 - - - +
487A TRP* 1.3 77.7 - - - +
489A ASN* 1.3 86.5 + - - +
490A GLY 3.3 1.8 - - - -
491A GLU* 2.9 28.0 + - + +
493A LYS* 6.3 1.8 - - - +
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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