Contacts of the helix formed by residues 414 - 424 (chain A) in PDB entry 1L8A
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 MET 414 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASP* 1.3 67.0 + - - +
416A GLY 3.2 5.1 - - - +
417A VAL* 3.6 29.8 - - + +
418A ARG* 2.9 30.5 + - + +
433A ILE* 3.9 32.5 - - + +
434A GLU* 4.0 30.1 - - + +
436A LEU* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ASP* 4.5 1.3 - - - +
414A MET* 1.3 83.0 - - - +
416A GLY* 1.3 57.0 + - - +
418A ARG* 3.5 11.0 + - - +
419A HIS* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A MET 5.5 0.2 - - - +
398A ASP* 3.3 22.5 - - - +
414A MET 3.2 2.8 - - - +
415A ASP* 1.3 79.7 - - - +
417A VAL* 1.3 61.0 + - - +
419A HIS* 3.3 3.3 + - - +
420A ILE* 3.1 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TRP* 3.5 26.9 - - + -
90A ILE* 5.6 2.7 - - + -
91A MET* 4.3 11.9 - - + -
94A LEU* 4.9 16.2 - - + -
414A MET* 3.4 35.4 + - - +
415A ASP 3.3 0.2 - - - -
416A GLY* 1.3 74.8 - - - +
418A ARG* 1.3 63.3 + - - +
420A ILE* 3.4 10.1 + - - +
421A ARG* 3.1 21.0 + - - +
433A ILE* 3.9 11.7 - - + -
436A LEU* 4.5 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A MET* 2.9 18.8 + - + +
415A ASP* 3.7 11.2 - - - +
416A GLY 3.3 0.2 - - - -
417A VAL* 1.3 75.1 - - - +
419A HIS* 1.3 64.1 + - - +
421A ARG* 3.3 25.2 + - - +
422A ASP* 3.0 44.6 + - - +
430A ASP* 3.5 23.0 + - - +
433A ILE* 3.4 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLY* 3.0 33.7 + - - -
396A MET 3.7 15.0 + - - -
397A GLY* 3.8 7.0 + - - -
398A ASP* 3.8 20.4 - - - +
415A ASP 3.0 14.4 + - - +
416A GLY 3.3 8.7 - - - +
418A ARG* 1.3 77.5 - - - +
420A ILE* 1.3 57.9 + - - +
422A ASP* 3.3 7.8 + - - +
423A ARG* 2.7 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 5.1 0.7 - - + -
87A TRP* 3.4 36.8 - - + +
90A ILE* 3.5 38.6 - - + -
395A GLY 4.3 9.6 - - - +
396A MET* 4.8 11.7 - - + +
416A GLY 3.1 17.7 + - - +
417A VAL* 3.6 10.5 - - - +
419A HIS* 1.3 80.5 - - - +
421A ARG* 1.3 69.6 + - - +
423A ARG* 3.7 8.7 - - - -
424A PHE* 3.0 39.3 + - + +
426A VAL* 4.0 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TRP* 3.7 24.7 - - + -
417A VAL 3.1 10.6 + - - +
418A ARG* 3.4 37.1 - - - +
420A ILE* 1.3 81.7 - - - +
422A ASP* 1.3 83.1 + - - +
425A ASN* 3.0 7.0 + - - -
426A VAL* 2.8 55.6 + - + +
428A VAL* 2.8 35.3 + - + +
429A SER 3.9 7.7 + - - -
430A ASP* 3.0 30.5 + - - +
433A ILE* 4.2 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ARG* 3.0 34.7 + - - +
419A HIS* 3.6 5.7 - - - +
421A ARG* 1.3 103.9 + - - +
423A ARG* 1.3 66.6 + - - +
425A ASN* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.1 24.1 + - - +
360A ASN* 5.6 0.4 - - - +
394A TYR* 3.1 37.2 + - - -
395A GLY* 3.7 18.6 - - - +
419A HIS* 2.7 34.8 + - + +
420A ILE* 3.6 9.2 - - - +
422A ASP* 1.3 74.2 - - - +
424A PHE* 1.3 84.5 + - + +
425A ASN* 4.0 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.5 24.2 + - - +
83A SER* 3.0 33.6 + - - +
86A ARG* 3.6 37.7 - - + -
90A ILE* 6.0 0.4 - - + -
111A GLN* 4.3 7.0 - - - -
394A TYR* 3.8 27.6 - + - -
395A GLY* 3.7 26.2 - - - -
420A ILE* 3.0 35.5 + - + +
423A ARG* 1.3 100.6 - - + +
425A ASN* 1.3 73.4 + - - +
426A VAL* 3.2 8.1 + - + -
----------------------------------------------------------
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