Contacts of the helix formed by residues 379 - 394 (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 SER 379 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A THR* 2.9 19.8 + - - +
378A ASN* 1.3 82.0 + - - +
380A SER* 1.3 57.6 + - - +
381A TRP* 3.4 9.7 + - - +
382A LEU* 2.9 20.2 + - - -
383A TRP 3.0 21.8 + - - -
399A ARG* 4.5 2.2 - - - -
443A PRO 3.8 17.9 - - - -
444A LYS* 3.6 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ASN 4.3 0.6 + - - -
379A SER* 1.3 68.7 - - - +
381A TRP* 1.3 60.4 + - - +
383A TRP* 3.6 2.8 - - - +
384A ASN* 2.8 42.8 + - - -
399A ARG* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A VAL* 4.0 17.9 - - + -
379A SER* 3.2 6.8 + - - +
380A SER* 1.3 77.9 - - - +
382A LEU* 1.3 82.7 + - + +
384A ASN* 3.1 6.1 + - + +
385A LYS* 3.1 61.0 + - + +
444A LYS* 3.6 37.9 - - + +
478A PHE* 5.6 0.2 - + - -
482A PHE* 3.5 30.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A VAL* 4.4 8.3 - - + -
355A ILE* 4.1 15.0 - - + -
377A THR* 3.9 5.4 - - - +
379A SER* 2.9 20.1 + - - +
381A TRP* 1.3 86.5 - - + +
383A TRP* 1.3 64.3 + - - +
385A LYS* 3.2 1.9 + - - -
386A LEU* 3.1 50.2 + - + +
444A LYS* 3.9 24.7 - - + +
445A TRP 3.7 17.3 - - - +
446A ALA* 3.6 26.0 - - + +
478A PHE* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL* 3.2 36.8 - - + -
377A THR* 3.7 12.7 - - + +
379A SER 3.0 11.2 + - - +
380A SER* 3.6 11.4 - - - +
381A TRP 3.3 0.2 - - - -
382A LEU* 1.3 79.1 - - - +
384A ASN* 1.3 72.1 + - - +
386A LEU* 3.3 5.0 + - + +
387A PHE* 2.8 58.1 + + + +
397A VAL* 3.4 26.0 - - + -
398A TRP* 3.8 7.0 - + - -
399A ARG* 3.3 59.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A SER* 2.8 33.4 + - - +
381A TRP* 3.1 6.9 + - + +
383A TRP* 1.3 87.2 + - - +
385A LYS* 1.3 65.9 + - + +
387A PHE* 3.7 10.7 - - - +
388A GLU* 2.9 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A TRP* 3.1 63.1 + - + +
382A LEU 3.2 5.1 + - - +
384A ASN* 1.3 78.9 - - + +
386A LEU* 1.3 57.8 + - - +
388A GLU* 3.8 23.3 + - - +
389A ALA* 3.0 27.2 + - - +
478A PHE* 3.8 24.4 - - + -
481A ARG* 5.5 6.1 - - - -
482A PHE* 5.6 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ILE* 4.7 6.5 - - + -
375A VAL* 5.2 5.2 - - + -
382A LEU* 3.1 52.1 + - + +
383A TRP* 3.8 7.6 - - + +
385A LYS* 1.3 71.7 - - - +
387A PHE* 1.4 68.2 + - - +
389A ALA* 3.2 7.9 - - - +
390A SER* 3.0 22.1 + - - -
397A VAL* 4.2 13.5 - - + -
446A ALA* 4.4 13.9 - - + -
448A LEU* 4.8 16.4 - - + -
474A THR* 4.0 11.8 - - + +
475A LEU* 4.2 22.7 - - + -
478A PHE* 4.1 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASN* 3.6 42.0 - - + -
383A TRP* 2.8 56.1 + + + +
384A ASN* 3.7 14.6 - - - +
386A LEU* 1.4 71.8 - - - +
388A GLU* 1.3 62.9 + - + +
390A SER* 2.7 30.6 + - - -
391A ILE* 3.1 36.3 + - + +
397A VAL* 3.7 12.9 - - + +
398A TRP* 6.0 2.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASN* 2.9 40.7 + - - +
385A LYS* 3.8 21.0 + - - +
387A PHE* 1.3 78.3 - - + +
389A ALA* 1.4 63.6 + - - +
391A ILE* 3.1 29.2 + - + +
392A GLU 3.5 4.3 + - - -
481A ARG* 3.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LYS 3.0 15.0 + - - +
386A LEU* 3.2 13.9 - - - +
388A GLU* 1.4 75.4 - - - +
390A SER* 1.3 57.3 + - - -
392A GLU* 3.4 12.3 + - - +
393A THR* 3.4 19.8 - - - +
474A THR* 3.5 25.8 - - + +
477A GLU* 3.8 10.9 - - + +
478A PHE* 3.8 19.3 - - + +
481A ARG* 4.6 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASN 4.3 6.5 + - - +
386A LEU 3.0 10.7 + - - -
387A PHE* 2.7 21.7 + - - -
389A ALA* 1.3 72.7 - - - +
391A ILE* 1.3 64.3 + - - +
393A THR* 3.4 8.7 - - - -
394A GLY* 3.1 23.9 + - - -
395A ASP 3.3 23.6 + - - -
396A ARG* 3.8 9.3 + - - +
397A VAL* 3.4 21.6 + - - +
474A THR* 3.8 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 4.0 34.5 - - + -
81A ASN* 3.9 15.9 - - - +
82A TRP* 3.5 12.0 - - - +
83A HIS* 2.9 38.8 + - + +
387A PHE* 3.1 42.9 + - + +
388A GLU* 3.1 17.7 + - + +
390A SER* 1.3 80.5 - - - +
392A GLU* 1.3 62.5 + - + +
394A GLY 4.0 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 5.8 1.9 - - - +
83A HIS* 4.0 11.6 + - - +
86A LYS* 3.4 46.3 + - - +
90A ARG* 3.1 17.7 + - - -
388A GLU 3.5 1.0 + - - +
389A ALA 3.4 10.5 + - - +
390A SER 3.3 0.4 - - - -
391A ILE* 1.3 81.7 - - + +
393A THR* 1.3 58.7 + - + +
394A GLY 3.4 0.2 - - - -
477A GLU* 4.3 16.6 - - + +
481A ARG* 3.0 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 3.8 1.0 - - - +
90A ARG* 3.4 17.6 + - - +
160A PHE* 5.2 3.4 - - + -
389A ALA 3.4 13.0 + - - +
390A SER* 3.4 6.1 - - - -
392A GLU* 1.3 78.1 - - + +
394A GLY* 1.3 58.3 + - - +
395A ASP* 3.1 12.2 + - - -
473A ARG* 2.9 73.9 + - + +
474A THR* 3.1 16.3 + - - -
477A GLU* 3.7 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TRP* 3.5 37.4 - - - -
83A HIS 5.6 0.4 - - - -
87A GLU* 3.8 18.4 - - - +
90A ARG* 4.4 0.4 - - - +
390A SER 3.1 10.7 + - - -
391A ILE 4.0 1.2 + - - -
392A GLU 3.4 2.2 - - - -
393A THR* 1.3 78.3 + - - +
395A ASP* 1.3 58.5 + - - +
396A ARG* 3.3 9.4 + - - -
462A TYR* 4.9 2.3 + - - -
470A ARG* 5.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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