Contacts of the strand formed by residues 466 - 473 (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 TYR 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A THR* 6.5 0.2 - - + -
193A PRO* 3.4 25.1 + - + +
194A SER 3.6 10.4 + - - -
195A ASP* 4.9 0.2 + - - -
197A GLN* 3.7 23.0 - - + +
198A GLN* 3.3 42.4 + - + +
201A ALA* 4.7 4.0 - - + -
327A ILE* 3.5 28.9 - - + -
328A LYS 3.0 10.8 - - - +
329A LEU* 3.4 28.9 - - + -
330A GLN* 4.8 2.1 + - - -
465A ARG* 1.3 81.5 - - - +
467A GLU* 1.3 65.0 + - - +
468A ILE* 4.9 1.6 - - + -
486A SER* 3.3 6.6 - - - -
487A TRP* 2.9 60.0 + + + +
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Residues in contact with GLU 467 (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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327A ILE* 3.6 2.4 - - - -
328A LYS* 2.7 54.2 + - + +
330A GLN* 3.8 42.3 + - + +
331A SER 5.5 0.9 - - - -
466A TYR* 1.3 77.2 - - - +
468A ILE* 1.3 63.7 + - - +
469A MET* 3.4 19.9 - - + +
483A ASN* 3.4 18.8 - - - +
485A GLY 3.6 6.3 - - - +
486A SER* 4.2 2.5 - - - +
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Residues in contact with ILE 468 (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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201A ALA* 6.2 0.9 - - + -
205A ILE* 3.6 22.7 - - + -
325A ILE* 3.9 22.9 - - + -
326A THR 3.4 8.3 - - - +
327A ILE* 4.6 5.2 - - + -
466A TYR* 4.6 2.2 - - + +
467A GLU* 1.3 75.4 - - - +
469A MET* 1.3 66.8 + - - +
484A VAL* 2.8 28.6 + - + -
485A GLY* 3.0 15.8 + - - +
486A SER* 3.5 35.7 - - - +
487A TRP* 3.8 9.0 - - + +
492A LEU* 3.9 17.5 - - + -
494A MET* 4.0 21.8 - - + -
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Residues in contact with MET 469 (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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309A ASP* 4.4 18.2 - - + +
325A ILE* 3.4 10.7 - - - +
326A THR* 2.7 54.0 + - - +
328A LYS* 4.4 18.6 - - + -
467A GLU* 3.4 28.5 - - + +
468A ILE* 1.3 91.4 - - - +
470A ASN* 1.3 61.2 + - - +
481A TYR* 4.4 23.1 - - + +
482A ILE 3.4 6.1 - - - +
483A ASN* 3.1 43.1 - - + +
484A VAL* 4.8 0.4 - - - -
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Residues in contact with ASN 470 (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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323A GLY* 3.5 12.1 - - - +
324A GLY 2.8 18.3 - - - +
325A ILE* 4.0 9.0 - - + +
469A MET* 1.3 75.8 - - - +
471A PHE* 1.3 64.8 + - - +
472A LYS* 3.7 22.3 + - - +
480A ASP 3.4 2.3 - - - +
481A TYR* 3.3 3.4 - - - -
482A ILE* 2.7 39.6 + - + +
484A VAL* 3.4 28.6 - - + +
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Residues in contact with PHE 471 (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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307A TRP* 4.6 5.8 - - + -
311A TYR* 5.6 2.5 - + - -
314A THR* 3.8 21.5 - - + -
318A GLN* 3.4 49.8 - - + -
321A ALA* 3.7 14.4 - - + -
322A VAL* 3.6 17.9 - - - -
323A GLY* 2.8 30.8 + - - -
324A GLY 2.9 20.1 + - - +
326A THR* 5.8 1.2 - - + +
470A ASN* 1.3 71.2 + - - +
472A LYS* 1.3 60.0 + - - +
479A PHE* 3.7 20.9 - + + -
480A ASP* 3.7 10.8 - - - -
481A TYR* 3.5 43.4 - + + -
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Residues in contact with LYS 472 (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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322A VAL* 4.0 8.1 - - + -
323A GLY* 5.2 1.8 - - - +
470A ASN* 3.9 23.8 - - - +
471A PHE* 1.3 78.1 - - - +
473A GLU* 1.3 65.0 + - - +
474A MET* 3.6 22.6 + - + +
479A PHE* 3.3 6.9 - - - -
480A ASP 3.0 31.3 + - - +
482A ILE* 3.7 27.1 - - + -
484A VAL* 5.8 0.2 - - + -
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Residues in contact with GLU 473 (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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322A VAL* 3.8 8.6 - - + +
472A LYS* 1.3 77.0 - - - +
474A MET* 1.3 64.9 + - - +
475A GLY 3.3 13.4 + - - +
477A ASP 5.7 0.4 - - - +
478A TYR 3.1 9.4 - - - +
479A PHE* 3.6 26.6 - - + -
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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