Contacts of the helix formed by residues 396 - 410 (chain A) in PDB entry 1L2L
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 396 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLY* 6.0 1.3 - - - -
394A PRO 4.6 0.2 - - - -
395A ILE* 1.3 70.9 - - - +
397A GLU* 1.3 75.2 + - - -
398A GLN* 3.2 4.9 - - - -
399A GLY* 3.0 10.1 + - - -
400A LEU* 2.9 20.3 - - - +
429A THR* 3.0 21.0 + - - -
430A LYS 3.2 12.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ILE 3.6 5.2 + - - +
396A GLY* 1.3 78.2 - - - -
398A GLN* 1.3 72.7 + - + +
400A LEU* 3.1 21.7 + - - +
401A GLU* 3.2 19.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ASP* 3.7 23.9 + - - +
320A PRO* 4.0 32.1 - - + +
347A TYR* 4.2 19.9 - - - +
348A GLY* 4.6 9.4 - - - -
396A GLY* 5.1 1.6 - - - -
397A GLU* 1.3 87.2 - - + +
399A GLY* 1.3 62.6 + - - +
401A GLU* 3.3 9.3 + - - +
402A VAL* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLY* 3.3 25.0 + - - -
396A GLY* 3.0 12.3 + - - -
398A GLN* 1.3 79.7 - - - +
400A LEU* 1.3 60.5 + - - +
402A VAL* 2.8 23.0 - - - +
403A GLU* 3.2 5.5 + - - +
426A PHE* 3.2 9.4 - - - -
428A PRO* 4.1 14.1 - - - -
429A THR 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 6.1 3.4 - - + -
395A ILE* 3.4 27.1 - - + +
396A GLY 2.9 29.2 - - - +
397A GLU* 3.1 10.2 + - - +
399A GLY* 1.3 73.5 - - - +
401A GLU* 1.3 72.7 + - - +
403A GLU* 3.3 16.5 + - - +
404A LYS* 3.1 22.5 + - - +
428A PRO* 4.8 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PRO* 6.1 2.7 - - + -
397A GLU* 3.2 16.6 + - + +
398A GLN* 3.3 10.5 + - - +
400A LEU* 1.3 83.8 - - - +
402A VAL* 1.3 62.2 + - - +
404A LYS* 3.4 22.5 + - - +
405A ILE* 3.2 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PRO* 5.2 6.5 - - + +
323A PRO* 3.8 28.9 - - + -
349A TYR* 3.8 28.7 - - + -
398A GLN 3.1 15.0 + - - +
399A GLY* 2.8 31.2 - - - +
401A GLU* 1.3 73.9 - - - +
403A GLU* 1.3 65.4 + - - +
405A ILE* 3.0 13.0 + - + +
406A LEU* 2.9 27.1 + - + +
426A PHE* 3.4 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 2.8 43.3 + - - -
399A GLY 3.2 3.8 + - - +
400A LEU* 3.5 19.7 - - - +
401A GLU 3.3 0.2 - - - -
402A VAL* 1.3 81.5 - - - +
404A LYS* 1.3 62.9 + - - +
406A LEU* 3.2 5.6 + - - +
407A GLU* 2.9 56.3 + - + +
412A LEU* 5.6 1.6 - - + -
414A ASP* 5.6 1.0 - - - -
415A GLY* 5.0 3.7 + - - -
426A PHE* 3.2 29.6 - - + -
428A PRO* 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LEU 3.1 12.7 + - - +
401A GLU* 3.4 28.6 + - - +
403A GLU* 1.3 76.7 - - - +
405A ILE* 1.3 62.5 + - + +
407A GLU* 3.4 16.1 + - - +
408A LYS* 3.3 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PRO* 3.6 24.2 - - + -
324A ILE* 3.4 32.5 - - + -
401A GLU* 3.3 16.4 - - + +
402A VAL* 3.0 12.5 + - + +
404A LYS* 1.3 78.0 - - + +
406A LEU* 1.3 62.2 + - + +
408A LYS* 3.1 28.8 + - + +
409A GLU* 3.3 8.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PRO* 4.0 15.3 - - + -
324A ILE* 5.3 2.9 - - + +
327A ILE* 3.6 29.2 - - + -
351A LEU* 3.7 18.8 - - + -
402A VAL* 2.9 26.0 + - + +
403A GLU 3.9 2.5 - - - +
405A ILE* 1.3 72.6 - - + +
407A GLU* 1.3 59.6 + - - +
408A LYS 3.1 2.5 - - - -
409A GLU* 3.8 3.4 - - + +
410A PHE* 2.8 44.3 + - + +
412A LEU* 3.4 18.0 - - + +
424A LEU* 5.1 2.5 - - + -
426A PHE* 3.6 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A GLU* 2.9 55.8 + - + +
404A LYS* 3.8 10.2 + - - +
405A ILE 3.2 0.2 - - - -
406A LEU* 1.3 77.0 - - - +
408A LYS* 1.3 61.6 + - + +
410A PHE 3.0 17.3 - - - +
412A LEU* 4.1 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LYS* 3.3 31.8 - - - +
405A ILE* 3.1 15.5 + - + +
406A LEU 3.1 0.4 - - - -
407A GLU* 1.3 79.8 - - + +
409A GLU* 1.3 60.2 + - - +
410A PHE 5.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ILE* 4.7 24.1 - - + +
405A ILE* 3.3 10.5 + - + +
406A LEU* 4.2 3.1 - - + +
408A LYS* 1.3 83.0 - - + +
410A PHE* 1.3 92.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ILE* 6.4 0.9 - - + -
327A ILE* 3.8 40.2 - - + -
406A LEU* 2.8 27.6 + - + +
407A GLU 3.0 21.7 - - - +
408A LYS 5.3 0.2 - - - -
409A GLU* 1.3 102.7 - - + +
411A SER* 1.3 62.0 + - - +
412A LEU* 3.1 20.2 + - + -
418A SER 3.8 19.7 - - - +
419A ILE* 4.1 29.4 - - + -
424A LEU* 3.9 16.6 - - + -
----------------------------------------------------------
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