Contacts of the helix formed by residues 471 - 484 (chain A) in PDB entry 1LAP
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 PRO 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A THR* 4.0 17.3 - - + -
373A THR* 3.6 27.1 - - + -
395A ASP* 3.3 18.2 - - - +
397A VAL* 5.5 0.7 - - + -
448A LEU* 3.9 19.1 - - + -
450A ILE* 3.5 22.7 - - + -
470A ARG* 1.4 78.6 - - - +
472A THR* 1.4 52.5 + - - +
473A ARG 3.3 2.7 - - - -
474A THR* 2.7 40.9 + - + +
475A LEU* 3.4 11.2 + - + +
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Residues in contact with THR 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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163A GLY 3.8 22.9 - - - +
164A GLN* 4.0 8.3 - - - +
167A ALA* 3.9 8.0 - - - +
279A THR* 3.5 16.7 + - - +
282A SER* 4.0 13.7 - - - -
283A ALA* 4.1 8.2 - - - +
395A ASP* 4.5 0.2 + - - -
469A GLY 2.7 23.9 + - - -
471A PRO* 1.4 72.2 - - - +
473A ARG* 1.3 60.9 + - - +
475A LEU* 3.3 13.7 + - - +
476A ILE* 3.1 37.3 + - + +
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Residues in contact with ARG 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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90A ARG* 3.6 5.5 - - - +
121A GLU* 3.1 29.9 + - - -
125A LEU* 4.0 11.6 - - - +
160A PHE* 3.6 44.0 - - + +
161A ALA* 4.4 1.6 - - - +
164A GLN* 3.1 27.6 + - + +
393A THR* 2.9 52.1 + - + +
395A ASP* 4.3 17.0 + - + +
462A TYR* 3.1 27.5 + - - -
471A PRO 3.1 1.0 + - - -
472A THR* 1.3 74.8 - - - +
474A THR* 1.3 59.5 + - - +
476A ILE* 4.0 8.0 - - + +
477A GLU* 3.0 31.4 + - - +
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Residues in contact with THR 474 (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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386A LEU* 4.0 31.2 - - + +
389A ALA* 3.5 5.8 - - + +
390A SER* 3.8 9.9 - - - -
393A THR* 3.1 19.4 + - - -
395A ASP* 2.9 26.4 + - - +
397A VAL* 4.3 15.9 - - + -
448A LEU* 6.0 0.2 - - + -
471A PRO* 2.7 20.7 + - + -
473A ARG* 1.3 72.5 - - - +
475A LEU* 1.3 61.2 + - + +
477A GLU* 4.4 0.4 - - - -
478A PHE* 2.8 30.1 + - - +
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Residues in contact with LEU 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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247A PHE* 4.1 19.3 - - + -
279A THR* 3.6 37.0 - - + +
280A ILE* 4.9 3.8 - - + -
283A ALA* 4.0 11.2 - - + -
355A ILE* 4.9 10.8 - - + -
357A ALA* 5.6 0.7 - - + -
386A LEU* 4.2 15.5 - - + -
448A LEU* 4.0 24.5 - - + -
471A PRO* 3.4 20.7 + - + +
472A THR* 3.5 9.9 - - - +
473A ARG 3.2 0.2 - - - -
474A THR* 1.3 81.5 - - + +
476A ILE* 1.3 63.7 + - - +
478A PHE* 3.2 8.0 + - + +
479A LEU* 3.0 29.4 + - - +
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Residues in contact with ILE 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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160A PHE* 3.9 37.0 - - + +
163A GLY* 4.7 0.2 - - - -
283A ALA* 3.8 13.2 - - - +
286A SER* 3.6 36.8 - - - +
287A ALA* 5.1 1.8 - - - +
290A LEU* 3.8 28.0 - - + -
292A LEU* 4.7 2.0 - - + +
472A THR* 3.1 32.1 + - + +
473A ARG* 4.0 11.2 - - - +
475A LEU* 1.3 73.6 - - - +
477A GLU* 1.3 52.7 + - - +
479A LEU* 3.1 11.9 + - - +
480A PHE* 2.8 33.0 + - - +
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Residues in contact with GLU 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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117A GLN* 5.0 2.9 + - - +
160A PHE* 3.3 24.3 - - + -
389A ALA* 3.8 25.8 - - - +
392A GLU* 4.3 14.5 - - + +
393A THR* 3.7 12.5 - - + +
473A ARG 3.0 19.8 + - - +
474A THR 3.8 3.1 - - - +
476A ILE* 1.3 75.1 - - - +
478A PHE* 1.3 61.7 + - - +
480A PHE* 3.2 18.8 + - - +
481A ARG* 2.9 55.8 + - - +
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Residues in contact with PHE 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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245A LEU* 4.1 20.9 - - + -
247A PHE* 4.6 6.5 - + - -
353A VAL* 4.5 2.9 - - + -
355A ILE* 3.6 28.3 - - + -
381A TRP* 5.6 0.2 - + - -
382A LEU* 3.9 17.0 - - + -
385A LYS* 3.8 34.1 - - + -
386A LEU* 4.1 19.1 - - + -
389A ALA* 3.8 12.3 - - + +
474A THR 2.8 22.4 + - - +
475A LEU* 3.2 11.0 + - + +
477A GLU* 1.3 71.8 - - - +
479A LEU* 1.3 65.8 + - + +
481A ARG* 3.4 5.2 + - - +
482A PHE* 3.0 55.0 + + - +
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Residues in contact with LEU 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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245A LEU* 3.9 26.9 - - + -
247A PHE* 3.8 33.4 - - + -
283A ALA* 4.1 13.0 - - + +
284A ILE* 5.2 0.4 - - - -
287A ALA* 4.0 11.9 - - + -
292A LEU* 3.9 14.1 - - + +
294A ILE* 4.2 8.3 - - + +
296A ILE* 3.9 32.3 - - + -
475A LEU 3.0 17.7 + - - +
476A ILE* 3.4 7.6 - - - +
478A PHE* 1.3 73.9 - - + +
480A PHE* 1.3 67.6 + - - +
482A PHE* 3.1 4.2 + - + +
483A SER* 2.8 26.7 + - - -
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Residues in contact with PHE 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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156A ARG* 4.7 22.9 - - - -
160A PHE* 4.8 6.3 - + + -
290A LEU* 4.8 10.3 - - + -
292A LEU* 3.8 23.5 - - + +
476A ILE 2.8 16.6 + - - +
477A GLU* 3.2 35.4 - - - +
479A LEU* 1.3 71.3 - - - +
481A ARG* 1.3 66.3 + - + +
483A SER* 2.8 20.3 + - - -
484A GLN* 3.1 50.9 - - - +
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Residues in contact with ARG 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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385A LYS* 5.5 6.1 - - - -
388A GLU* 3.9 38.8 + - - +
389A ALA* 4.6 7.4 - - - +
392A GLU* 3.0 36.8 - - - +
477A GLU* 2.9 36.6 + - - +
478A PHE* 3.9 4.7 - - - +
480A PHE* 1.3 80.7 - - + +
482A PHE* 1.3 62.4 + - - +
484A GLN* 2.9 30.1 + - + +
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Residues in contact with PHE 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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245A LEU* 4.1 26.7 - - + -
294A ILE* 4.5 10.7 - - + +
352A LYS* 3.9 37.5 - - + -
353A VAL* 4.6 6.5 - - + -
381A TRP* 3.5 34.5 - + - -
385A LYS* 5.6 4.7 - - + +
478A PHE* 3.0 38.7 + + + +
479A LEU* 3.1 8.5 + - + +
481A ARG* 1.3 74.6 - - - +
483A SER* 1.3 58.4 + - - +
484A GLN 2.9 15.1 - - - +
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Residues in contact with SER 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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292A LEU* 3.3 18.2 - - - +
293A PRO* 3.7 30.3 - - - +
294A ILE* 3.6 35.7 - - - -
479A LEU 2.8 12.4 + - - -
480A PHE* 2.8 15.6 + - - -
482A PHE* 1.3 71.2 - - - +
484A GLN* 1.3 65.9 + - - +
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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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480A PHE* 3.1 54.1 + - - +
481A ARG* 2.9 19.5 + - - +
482A PHE 2.9 10.9 - - - +
483A SER* 1.3 86.5 - - - +
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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