Contacts of the strand formed by residues 472 - 484 (chain A) in PDB entry 1LMU
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 GLU 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A PRO* 4.0 19.6 - - - +
273A PRO* 4.7 17.6 - - + +
274A ALA 3.5 5.6 - - - +
275A LEU* 4.2 15.5 - - + -
470A GLY 3.4 3.5 + - - +
471A ASP* 1.4 74.0 - - - +
473A LEU* 1.3 65.6 + - - +
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Residues in contact with LEU 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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228A ILE* 3.5 11.7 - - + -
229A VAL 3.3 10.1 - - - +
230A THR* 3.4 31.0 - - + +
231A PRO* 4.6 3.1 - - + -
236A PHE* 3.6 28.9 - - + -
273A PRO* 3.5 7.3 - - - +
274A ALA* 2.6 38.8 + - + +
276A VAL* 3.0 35.0 - - + -
427A LEU* 4.9 1.8 - - + -
467A VAL* 3.9 13.7 - - + -
471A ASP* 3.6 13.7 - - + +
472A GLU* 1.3 81.1 - - - +
474A LEU* 1.3 59.9 + - - +
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE* 3.3 4.8 - - - -
229A VAL* 2.8 48.6 + - + +
231A PRO* 5.6 0.2 - - - +
271A GLY* 3.2 26.9 - - - +
272A GLN 3.3 13.7 - - - +
273A PRO* 4.0 9.0 - - + -
274A ALA 4.2 0.7 - - - +
473A LEU* 1.3 77.8 - - - +
475A CYS* 1.4 77.4 + - - +
476A GLU* 3.0 22.4 + - + +
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Residues in contact with CYS 475 (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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226A ALA* 3.5 22.4 - - - -
227A HIS 3.4 9.6 - - - -
228A ILE* 3.5 11.4 - - + +
269A ILE* 3.2 39.9 - - + +
271A GLY* 3.1 19.4 + - - -
272A GLN 3.0 19.0 + - - +
274A ALA 4.4 1.2 - - - +
429A ILE* 4.3 6.5 - - + -
473A LEU 4.3 0.4 + - - -
474A LEU* 1.4 75.0 - - - +
476A GLU* 1.3 65.5 + - - +
477A LYS* 3.8 14.6 - - - -
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Residues in contact with GLU 476 (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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227A HIS* 2.8 19.5 + - + +
229A VAL* 3.6 27.1 - - + +
235A ARG* 3.1 46.6 + - - +
270A ASN* 3.4 13.2 + - - +
271A GLY* 4.0 1.9 + - - -
474A LEU* 3.0 14.3 + - + +
475A CYS* 1.3 73.9 - - - +
477A LYS* 1.3 67.3 + - + +
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Residues in contact with LYS 477 (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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227A HIS* 2.9 68.0 + - + +
270A ASN* 3.6 20.6 - - - +
475A CYS* 3.4 9.8 - - - -
476A GLU* 1.3 84.5 - - + +
478A GLY* 1.3 67.8 + - - +
479A GLU* 4.3 11.2 + - - -
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Residues in contact with GLY 478 (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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224A VAL* 5.5 0.9 - - - -
225A LYS 3.7 7.0 - - - -
226A ALA* 4.4 2.5 - - - -
227A HIS* 4.5 0.2 - - - -
266A VAL* 3.4 26.1 - - - +
269A ILE* 4.2 13.2 - - - -
270A ASN* 4.0 10.5 + - - +
477A LYS* 1.3 87.2 - - - +
479A GLU* 1.3 64.1 + - - +
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Residues in contact with GLU 479 (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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224A VAL* 3.6 3.8 - - - +
225A LYS* 3.1 60.2 + - + +
227A HIS* 3.7 24.4 + - - +
266A VAL* 4.0 5.1 - - - +
477A LYS* 4.3 10.5 + - - -
478A GLY* 1.3 76.0 - - - +
480A VAL* 1.4 75.5 + - - +
481A VAL* 3.6 8.8 + - + +
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Residues in contact with VAL 480 (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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222A PHE* 4.1 14.4 - - + -
223A GLU 3.6 3.4 - - - +
224A VAL* 4.9 0.4 - - - +
259A ARG* 3.0 36.5 + - - +
262A ALA* 3.7 21.1 - - + -
263A GLU* 3.9 27.8 - - + +
266A VAL* 3.5 24.5 - - + -
479A GLU* 1.4 80.1 - - - +
481A VAL* 1.3 62.7 + - - +
482A GLU* 3.7 3.3 + - - +
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Residues in contact with VAL 481 (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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222A PHE* 3.4 4.3 - - - -
223A GLU* 2.7 51.0 + - + +
225A LYS* 3.6 34.5 - - + +
479A GLU* 3.9 11.2 - - - +
480A VAL* 1.3 75.5 - - - +
482A GLU* 1.3 69.9 + - - +
483A ARG* 3.6 13.8 + - + +
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Residues in contact with GLU 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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220A ASP* 5.2 7.0 - - - +
222A PHE* 3.4 29.4 - - + -
259A ARG* 3.6 22.8 + - - +
480A VAL 3.7 3.4 + - - +
481A VAL* 1.3 77.5 - - - +
483A ARG* 1.3 59.7 + - - +
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Residues in contact with ARG 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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220A ASP* 3.4 8.2 - - - +
221A PHE* 2.9 78.7 + - + +
223A GLU* 3.5 24.5 + - + +
255A ARG* 5.1 5.3 - - - +
481A VAL* 4.7 12.8 - - + +
482A GLU* 1.3 75.5 - - - +
484A GLN* 1.3 70.8 + - - +
486A GLN* 6.1 1.3 - - - +
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Residues in contact with GLN 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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218A ALA* 3.2 33.7 - - - +
219A LYS 3.8 2.9 - - - -
220A ASP* 2.8 27.7 - - - +
221A PHE* 4.2 4.5 - - - -
483A ARG* 1.3 86.7 + - - +
485A THR* 1.3 67.3 + - - +
486A GLN* 3.8 22.1 + - + +
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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