Contacts of the helix formed by residues 416 - 432 (chain A) in PDB entry 3LLM
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 GLY 416 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388A LEU* 4.9 2.9 - - - -
390A VAL* 3.8 12.5 - - - +
414A GLY 3.4 0.4 - - - -
415A CYS* 1.3 75.3 - - - +
417A LYS* 1.3 63.3 + - - +
420A GLN* 3.0 35.5 + - - +
565A ADP 2.6 38.6 + - - -
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Residues in contact with LYS 417 (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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1A MN 4.3 5.8 + - - -
390A VAL* 4.7 2.2 - - + +
409A ILE* 4.3 16.2 - - + +
410A ARG 4.3 2.0 - - - -
411A GLY* 3.2 25.3 + - - +
412A ALA 3.2 18.8 + - - -
413A THR* 3.7 5.7 - - - +
415A CYS* 4.5 2.2 - - - -
416A GLY* 1.3 79.7 - - - +
418A THR* 1.3 66.9 + - - +
421A VAL* 3.1 34.4 + - + +
422A PRO* 3.8 0.2 - - - +
511A ASP* 5.3 1.1 - - - +
512A GLU* 5.1 3.6 - - - -
542A MSE 3.7 21.3 - - + +
543A SER 3.6 28.5 - - - +
544A ALA* 4.5 1.8 - - - +
563A VAL* 4.4 17.0 - - + -
565A ADP 2.6 40.4 + - - +
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Residues in contact with THR 418 (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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1A MN 2.2 28.5 + - - -
417A LYS* 1.3 79.9 - - - +
419A THR* 1.3 64.7 + - + +
422A PRO* 3.3 18.5 - - - +
444A GLN* 4.4 5.2 - - - +
453A VAL* 3.7 40.0 - - + +
457A VAL* 5.1 0.3 - - - +
488A PHE* 4.8 2.3 - - + -
511A ASP* 2.4 33.0 + - - +
512A GLU* 3.0 2.1 + - - +
542A MSE 4.9 1.8 - - - -
565A ADP 2.9 21.6 + - - +
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Residues in contact with THR 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 4.9 0.3 - - - +
416A GLY* 4.3 0.2 - - - -
418A THR* 1.3 80.4 - - + +
420A GLN* 1.3 78.1 + - - +
422A PRO* 4.3 2.0 - - - +
423A GLN* 2.9 29.1 + - - +
453A VAL* 4.8 5.6 - - + -
456A ARG* 4.0 25.6 - - + -
457A VAL* 4.0 16.0 - - + +
460A GLU* 3.9 8.2 + - - +
565A ADP 2.5 49.8 + - + +
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Residues in contact with GLN 420 (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 ARG* 2.7 37.1 + - - +
388A LEU* 3.7 26.8 - - + +
390A VAL* 4.0 11.0 - - + -
416A GLY 3.0 17.7 + - - +
419A THR* 1.3 99.9 + - - +
421A VAL* 1.3 69.7 + - - +
422A PRO* 3.2 2.7 - - - -
423A GLN* 2.7 17.2 + - - +
424A PHE* 2.9 32.8 + - + -
460A GLU* 2.5 32.9 + - - -
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Residues in contact with VAL 421 (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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390A VAL* 4.7 7.9 - - + -
397A ILE* 4.5 22.7 - - + -
401A ILE* 4.8 0.2 - - + -
409A ILE* 4.1 16.6 - - + -
417A LYS* 3.1 20.0 + - - +
420A GLN* 1.3 75.0 - - - +
422A PRO* 1.3 68.8 - - + +
424A PHE* 3.1 10.6 + - + +
425A ILE* 3.0 39.5 + - + +
509A ILE* 4.6 2.2 - - + -
540A VAL* 4.8 1.6 - - + -
542A MSE 2.8 39.5 - - + -
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Residues in contact with PRO 422 (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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417A LYS 3.8 1.1 - - - +
418A THR* 3.3 23.8 - - - +
419A THR 4.3 1.1 - - - -
420A GLN 3.3 3.8 - - - +
421A VAL* 1.3 93.8 - - + +
423A GLN* 1.3 57.2 + - + +
425A ILE* 3.3 1.2 + - + -
426A LEU* 3.0 25.5 + - - +
440A ILE* 3.6 13.2 - - + +
442A VAL* 4.3 13.0 - - + -
457A VAL* 5.9 0.9 - - + -
486A ILE* 3.8 29.6 - - + -
488A PHE* 4.6 8.7 - - + -
509A ILE* 4.1 25.4 - - + -
542A MSE 5.4 1.1 - - - -
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Residues in contact with GLN 423 (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 ARG* 3.3 30.2 + - - +
419A THR 2.9 23.2 + - - +
420A GLN 2.7 13.7 + - - +
422A PRO* 1.3 69.4 - - + +
424A PHE* 1.3 59.2 + - - +
426A LEU* 3.2 6.6 + - - +
427A ASP* 2.8 36.4 + - - +
457A VAL* 3.7 30.9 - - + +
460A GLU* 2.9 28.9 + - - +
461A ARG* 2.9 39.7 + - - +
486A ILE* 4.7 2.7 - - + -
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Residues in contact with PHE 424 (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 ARG* 3.6 25.8 - - - -
390A VAL* 4.3 22.7 - - + -
391A LYS* 4.1 32.1 - - + -
394A GLU* 3.6 50.9 - - + +
397A ILE* 4.7 10.1 - - + -
398A LEU* 3.5 16.1 - - + +
420A GLN* 2.9 36.4 + - + -
421A VAL* 3.6 14.1 - - + +
423A GLN* 1.3 75.3 - - - +
425A ILE* 1.3 62.8 + - + +
427A ASP* 4.3 3.8 - - + +
428A ASP* 3.0 25.8 + - - +
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Residues in contact with ILE 425 (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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397A ILE* 5.9 0.4 - - + -
398A LEU* 3.9 13.9 - - + -
401A ILE* 3.7 31.0 - - + -
421A VAL* 3.0 27.1 + - + +
422A PRO 3.6 4.3 - - - +
424A PHE* 1.3 79.2 - - + +
426A LEU* 1.3 65.3 + - - +
428A ASP* 3.4 1.8 + - + +
429A PHE* 3.3 29.0 + - + -
438A CYS* 4.5 0.9 - - - -
440A ILE* 3.7 13.2 - - + -
507A HIS* 3.4 39.9 - - + +
509A ILE* 4.2 17.5 - - + -
540A VAL* 4.8 2.7 - - + -
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Residues in contact with LEU 426 (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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422A PRO 3.0 17.3 + - - +
423A GLN* 3.6 5.4 - - - +
425A ILE* 1.3 75.4 - - - +
427A ASP* 1.3 57.4 - - - +
429A PHE* 3.2 6.2 + - - +
430A ILE* 2.9 39.3 + - + +
438A CYS* 4.1 17.3 - - + -
440A ILE* 4.0 2.4 - - + +
461A ARG* 3.5 32.5 - - - +
468A SER* 4.3 9.4 - - - -
481A ARG* 4.7 0.2 - - - +
484A ALA* 3.4 46.7 - - + +
485A SER* 3.8 6.3 - - - +
486A ILE* 4.2 18.8 - - + -
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Residues in contact with ASP 427 (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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368A LEU* 3.9 16.7 - - + +
385A ARG* 4.1 14.4 + - - -
394A GLU* 5.9 2.2 - - - +
423A GLN 2.8 23.1 + - - +
424A PHE* 4.3 4.0 - - + +
426A LEU* 1.3 69.4 - - - +
428A ASP* 1.3 58.8 + - - +
430A ILE* 3.9 5.6 - - - +
431A GLN* 2.9 35.4 + - + +
461A ARG* 2.7 42.6 + - - -
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Residues in contact with ASP 428 (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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398A LEU* 3.8 34.9 - - + +
402A SER* 6.1 0.9 - - - -
424A PHE 3.0 19.5 + - - +
425A ILE 3.6 5.2 - - - +
426A LEU 3.3 0.2 - - - -
427A ASP* 1.3 78.0 - - - +
429A PHE* 1.3 66.2 + - + +
431A GLN* 4.8 1.6 - - - -
432A ASN* 3.2 39.7 + - - +
434A ARG* 2.9 24.4 + - - -
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Residues in contact with PHE 429 (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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425A ILE* 3.3 19.8 + - + -
426A LEU 3.2 8.5 + - - +
428A ASP* 1.3 82.5 - - - +
430A ILE* 1.3 65.5 + - + +
432A ASN 3.4 4.5 + - - -
434A ARG* 2.9 83.3 + - + +
435A ALA* 3.9 3.4 - - - -
437A GLU* 3.6 27.6 - - + -
438A CYS* 3.6 24.7 - - + -
506A SER* 5.6 0.4 - - - -
507A HIS* 3.8 33.2 - + - -
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Residues in contact with ILE 430 (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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361A SER 4.9 1.0 - - - +
364A LEU* 4.3 6.1 - - + +
365A LYS* 3.7 39.0 - - + +
368A LEU* 3.7 27.8 - - + -
426A LEU* 2.9 42.1 + - + +
427A ASP* 3.9 17.3 - - - +
429A PHE* 1.3 76.5 - - + +
431A GLN* 1.3 65.2 + - - +
433A ASP* 3.3 9.9 + - - -
434A ARG 4.3 0.3 + - - -
435A ALA* 4.0 23.0 + - + -
461A ARG* 4.1 6.7 - - - +
481A ARG* 4.5 13.7 - - - +
484A ALA* 4.5 3.8 - - + -
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Residues in contact with GLN 431 (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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365A LYS* 3.2 41.2 + - - +
368A LEU* 5.2 9.6 - - + +
427A ASP* 2.9 19.2 + - + +
428A ASP* 4.1 3.4 - - - +
430A ILE* 1.3 79.0 - - + +
432A ASN* 1.3 64.4 + - - +
433A ASP 3.3 0.9 - - - -
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Residues in contact with ASN 432 (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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428A ASP* 3.2 31.6 + - - +
429A PHE 3.8 0.2 - - - -
430A ILE 3.3 0.4 - - - -
431A GLN* 1.3 85.3 - - - +
433A ASP* 1.3 72.3 + - - +
434A ARG* 3.3 31.5 + - - +
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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
------------------------------------------------------------
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