Contacts of the helix formed by residues 402 - 420 (chain A) in PDB entry 3LLK
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 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A TRP* 3.7 26.0 - - - -
393A CYS* 2.9 17.2 + - - +
395A GLY 4.6 0.6 - - - +
398A PRO 5.9 1.1 - - - -
400A PHE 3.3 3.6 + - - -
401A ARG* 1.3 80.1 - - - +
403A PHE* 1.3 67.4 + - - -
405A CYS* 3.0 13.7 + - - +
406A SER* 3.0 10.0 + - - -
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Residues in contact with PHE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ALA* 3.8 15.0 - - - -
310A TYR* 3.4 53.6 - + + -
311A ILE* 3.8 15.0 - - + -
315A GLU* 3.3 39.0 - - - -
390A TRP* 3.4 18.6 - + + +
401A ARG 3.6 0.2 + - - -
402A GLY* 1.3 70.3 - - - -
404A PRO* 1.4 64.2 - - + +
406A SER* 2.6 31.9 + - - -
407A LEU* 2.8 37.7 + - + +
447A PHE* 3.8 17.5 - + - -
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Residues in contact with PRO 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ARG 3.2 17.0 - - - +
403A PHE* 1.4 101.5 - - + +
405A CYS* 1.3 60.1 + - - +
407A LEU* 3.3 8.2 + - + +
408A TRP* 3.2 22.3 + - - -
447A PHE* 4.6 16.2 - - + -
449A CYS* 4.8 9.6 - - - -
452A CYS* 5.4 0.2 - - - -
550A FAD 3.5 41.0 + - - +
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Residues in contact with CYS 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLY 4.0 0.9 - - - -
393A CYS* 2.0 52.9 - - + -
401A ARG* 3.6 16.1 - - + -
402A GLY 3.0 15.9 + - - +
404A PRO* 1.3 78.6 - - - +
406A SER* 1.3 60.8 + - - +
407A LEU 3.3 0.3 + - - -
408A TRP* 3.3 5.0 + - - +
409A VAL* 3.1 25.3 + - - +
550A FAD 3.0 45.3 + - - +
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Residues in contact with SER 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASP* 3.7 16.9 - - - +
304A LEU* 5.0 1.6 - - - +
307A ALA* 3.4 16.5 - - - +
390A TRP* 3.3 34.5 - - - -
393A CYS* 3.2 10.5 - - - -
402A GLY 3.0 4.6 + - - -
403A PHE* 2.6 24.8 + - - -
405A CYS* 1.3 76.6 - - - +
407A LEU* 1.3 57.1 + - - +
409A VAL* 3.5 4.5 + - - +
410A LEU* 3.0 29.1 + - - +
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Residues in contact with LEU 407 (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 ALA* 5.1 0.9 - - + -
311A ILE* 4.0 26.7 - - + -
403A PHE* 2.8 30.0 + - + +
404A PRO* 3.6 7.9 - - + +
406A SER* 1.3 75.9 + - - +
408A TRP* 1.3 60.7 + - - +
410A LEU* 3.3 7.5 + - + +
411A PHE* 2.8 76.0 + - + -
442A TYR* 4.3 8.7 - - + -
447A PHE* 3.6 42.0 - - + -
550A FAD 4.4 4.0 - - + -
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Residues in contact with TRP 408 (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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404A PRO 3.2 10.7 + - - -
405A CYS 3.3 6.9 + - - +
407A LEU* 1.3 76.7 - - - +
409A VAL* 1.3 64.1 + - - +
411A PHE* 3.2 8.6 + + - +
412A HIS* 2.9 39.7 + + + -
456A PHE* 4.1 20.9 - + - -
459A MET* 4.9 0.2 - - + -
477A LEU* 3.8 25.1 - - + -
480A SER 4.8 1.3 - - - -
481A HIS* 3.3 66.3 + + + -
484A VAL* 4.2 13.9 - - + -
550A FAD 2.8 89.4 + + + +
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Residues in contact with VAL 409 (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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299A ILE* 4.2 23.1 - - + -
303A ASP* 5.8 6.3 - - + -
304A LEU* 4.0 17.7 - - + -
393A CYS* 4.2 12.6 - - - -
405A CYS 3.1 15.3 + - - +
406A SER* 3.7 7.4 - - - +
408A TRP* 1.3 75.9 - - - +
410A LEU* 1.3 64.0 + - - +
412A HIS* 3.4 3.2 + - - +
413A PHE* 3.0 23.0 + - + +
535A PHE* 4.1 20.9 - - + -
550A FAD 4.1 23.3 - - - +
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 4.0 15.2 - - + +
307A ALA* 4.2 13.5 - - + -
308A LEU* 4.3 10.1 - - + -
311A ILE* 3.6 30.7 - - + -
333A PHE* 4.3 11.0 - - + -
337A LEU* 4.1 3.6 - - + -
341A PHE* 3.7 34.1 - - + -
342A PRO* 5.7 0.7 - - + -
406A SER 3.0 17.9 + - - +
407A LEU* 3.6 9.4 - - + +
409A VAL* 1.3 75.6 - - - +
411A PHE* 1.3 64.5 + - + +
413A PHE* 3.2 4.7 + - + +
414A LEU* 2.9 45.5 + - + +
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Residues in contact with PHE 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A PHE* 3.7 29.4 - + - -
407A LEU* 2.8 60.5 + - + +
408A TRP* 3.6 12.8 - + + +
410A LEU* 1.3 76.5 - - + +
412A HIS* 1.3 62.5 + - - +
414A LEU* 3.1 5.9 + - + +
415A THR* 3.1 24.9 + - - +
439A ILE* 3.6 33.6 - - + +
442A TYR* 3.9 9.0 - + - -
443A VAL* 3.5 31.9 - - + -
456A PHE* 5.3 1.6 - + - -
477A LEU* 3.6 16.8 - - + -
550A FAD 4.5 12.8 - - + -
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Residues in contact with HIS 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TRP* 2.9 36.7 + + + +
409A VAL* 4.4 0.9 - - - -
411A PHE* 1.3 75.5 - - - +
413A PHE* 1.3 63.7 + - - +
415A THR* 2.7 23.9 + - - -
416A VAL* 3.0 13.0 + - - +
474A VAL 5.1 1.6 + - - -
477A LEU* 3.6 43.3 - - + +
478A TRP* 3.8 4.2 + - - +
481A HIS* 2.8 25.9 + - + -
531A LEU* 5.7 1.0 - - - +
535A PHE* 3.4 28.6 - + + -
550A FAD 3.1 38.9 - + - -
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Residues in contact with PHE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 4.2 16.6 - - + -
304A LEU* 4.5 8.7 - - + -
342A PRO* 3.5 29.2 - - + -
409A VAL* 3.0 17.2 + - + +
410A LEU* 3.5 9.0 - - + +
412A HIS* 1.3 79.0 - - - +
414A LEU* 1.3 57.0 + - + +
416A VAL* 3.2 1.6 + - - +
417A GLN* 2.9 56.1 + - + +
420A ARG* 3.8 0.4 - - - -
535A PHE* 3.6 42.6 - + + -
536A SER 3.3 26.7 - - - -
537A PRO 3.6 2.5 - - - -
540A ILE* 3.7 29.8 - - + -
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Residues in contact with LEU 414 (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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333A PHE* 4.0 21.8 - - + -
336A VAL* 4.0 16.6 - - + +
337A LEU* 3.9 25.6 - - + -
340A TYR* 3.8 25.9 - - + +
341A PHE* 3.9 19.3 - - - +
342A PRO* 5.4 1.1 - - + -
410A LEU* 2.9 30.3 + - + +
411A PHE* 3.1 11.2 + - + +
413A PHE* 1.3 77.4 - - + +
415A THR* 1.3 61.3 + - - +
417A GLN* 3.4 4.8 + - - +
418A ALA* 3.1 23.0 + - - +
435A VAL* 4.0 16.4 - - + +
439A ILE* 4.6 3.6 - - + -
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Residues in contact with THR 415 (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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411A PHE 3.1 12.3 + - - +
412A HIS* 2.7 24.6 + - - -
414A LEU* 1.3 74.9 - - - +
416A VAL* 1.3 62.8 + - - +
418A ALA* 3.3 6.4 + - - +
419A ALA* 3.1 16.3 + - - +
435A VAL* 4.1 10.8 - - + -
436A LEU* 3.9 21.5 - - + -
439A ILE* 4.1 6.3 - - + -
470A PRO 4.6 1.9 - - - +
473A ALA* 4.4 10.0 - - + +
474A VAL* 3.4 33.7 + - - +
477A LEU* 3.8 18.1 - - + +
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Residues in contact with VAL 416 (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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412A HIS* 3.0 16.5 + - + +
413A PHE 3.8 1.6 - - - +
415A THR* 1.3 76.3 - - - +
417A GLN* 1.3 66.0 + - - +
419A ALA* 2.9 12.7 + - - +
420A ARG* 3.0 39.0 + - - +
474A VAL* 3.8 27.8 - - + -
531A LEU 3.9 9.9 - - - +
532A LYS* 3.8 23.3 - - + -
535A PHE* 3.3 31.6 - - + +
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Residues in contact with GLN 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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339A LYS 5.6 0.4 + - - -
340A TYR* 2.8 49.5 + - + +
341A PHE 4.2 0.4 + - - -
342A PRO* 3.7 19.8 - - - +
413A PHE* 2.9 37.7 + - + +
414A LEU 3.7 4.9 - - - +
415A THR 3.4 0.2 - - - -
416A VAL* 1.3 75.2 - - - +
418A ALA* 1.3 62.2 + - - +
420A ARG* 2.9 49.3 + - - +
421A GLN* 4.5 1.6 - - - +
537A PRO* 3.8 10.8 - - - +
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Residues in contact with ALA 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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340A TYR* 3.7 20.6 - - + -
414A LEU 3.1 14.7 + - - +
415A THR* 3.6 6.7 - - - +
416A VAL 3.1 0.4 - - - -
417A GLN* 1.3 79.0 - - - +
419A ALA* 1.3 57.2 + - - +
421A GLN* 3.4 19.3 - - - +
432A ALA* 3.8 21.1 - - + +
435A VAL* 3.6 25.6 - - + -
470A PRO* 3.8 10.1 - - + +
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Residues in contact with ALA 419 (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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415A THR 3.1 12.0 + - - +
416A VAL* 2.9 10.6 + - + +
418A ALA* 1.3 74.6 - - - +
420A ARG* 1.3 56.9 + - - +
421A GLN 2.9 15.9 + - - +
470A PRO* 3.7 18.0 - - + +
471A ASN* 3.6 21.1 - - - +
474A VAL* 3.9 15.3 - - + -
532A LYS* 3.4 18.1 + - - +
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Residues in contact with ARG 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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413A PHE* 3.8 0.6 - - - -
416A VAL* 3.0 29.9 + - + +
417A GLN* 2.9 45.0 + - - +
419A ALA* 1.3 75.8 - - - +
421A GLN* 1.3 58.7 + - - +
532A LYS* 4.2 19.3 - - + +
535A PHE 2.6 24.5 + - - -
536A SER* 2.8 31.9 - - - +
537A PRO* 2.9 15.0 - - - +
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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
------------------------------------------------------------
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