Contacts of the helix formed by residues 443 - 454 (chain A) in PDB entry 4LOU
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 PRO 443 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLU* 5.1 0.4 - - - +
401A SER 3.8 6.3 - - - +
402A ILE 3.7 9.0 - - - +
403A ARG* 3.8 31.4 - - + +
442A LYS* 1.4 86.8 - - + +
444A LEU* 1.3 60.7 + - - +
445A TYR 4.9 0.2 - - - +
446A SER* 4.0 11.2 - - - +
447A ALA* 2.9 27.5 + - - +
25B LEU 5.3 2.0 - - - +
28B ARG* 3.5 56.8 - - + +
29B ASP* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A PHE* 5.4 0.9 - - + -
270A ASN* 3.4 31.0 - - + +
273A VAL* 4.0 22.7 - - + -
274A LEU* 4.6 8.1 - - + -
348A PHE* 4.6 10.1 - - + -
356A ILE* 4.1 33.0 - - + -
360A MET* 5.3 0.4 - - - -
401A SER* 3.0 24.3 + - - +
402A ILE* 3.9 14.4 - - + +
442A LYS 3.4 0.2 + - - -
443A PRO* 1.3 71.9 - - - +
445A TYR* 1.3 67.2 + - + +
447A ALA* 3.4 2.7 + - + -
448A ILE* 3.1 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER* 3.6 26.7 + - - -
109A ILE* 3.6 38.5 - - + +
110A PRO* 3.8 24.2 - - + +
113A GLU* 4.0 12.7 - - - +
149A GLY* 6.0 0.3 - - - -
199A PHE* 4.3 3.1 - + - -
203A GLU* 3.8 17.0 - - - +
348A PHE* 4.9 4.9 - + - -
355A GLY* 5.5 0.9 - - - -
356A ILE* 3.8 28.8 + - + +
357A PHE* 3.8 19.3 + + - +
402A ILE* 4.1 33.9 + - + +
443A PRO* 3.5 1.0 - - - +
444A LEU* 1.3 85.4 - - + +
446A SER* 1.3 57.8 + - - +
448A ILE* 5.2 2.7 - - + -
449A LEU* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU* 4.1 10.9 + - - -
203A GLU* 4.3 0.3 + - - -
443A PRO* 3.4 14.5 + - - +
444A LEU 3.3 0.2 - - - -
445A TYR* 1.3 80.4 - - - +
447A ALA* 1.3 58.0 + - - +
449A LEU* 4.5 4.5 - - - -
450A ALA* 3.2 25.3 + - - +
25B LEU* 3.6 35.6 - - - +
28B ARG* 3.1 36.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASN* 5.9 0.2 - - - +
274A LEU* 4.4 17.3 - - + +
442A LYS* 4.0 28.5 - - + +
443A PRO 2.9 18.1 + - - +
444A LEU* 3.4 4.9 + - + +
445A TYR 3.3 0.2 - - - -
446A SER* 1.3 77.4 - - - +
448A ILE* 1.3 59.8 + - - +
450A ALA* 4.1 7.4 - - - +
451A ARG* 3.2 29.1 + - - +
25B LEU 5.8 1.8 - - - +
26B LEU* 5.4 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO* 3.6 25.6 - - + -
273A VAL* 4.8 0.7 - - + -
274A LEU* 3.7 22.7 - - + -
277A GLN* 3.8 25.8 - - - +
348A PHE* 4.4 18.4 - - + -
444A LEU* 3.1 36.9 + - + +
445A TYR* 3.9 4.9 - - + +
447A ALA* 1.3 77.0 - - - +
449A LEU* 1.3 67.2 + - - +
450A ALA 3.2 1.1 - - - -
451A ARG* 3.2 6.4 + - - +
452A THR* 3.2 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO* 3.3 28.9 - - + +
111A GLU* 5.8 0.4 - - - +
113A GLU* 4.3 14.4 - - + +
114A GLY* 3.9 29.6 - - - +
117A GLU* 5.2 8.3 - - + -
120A ARG* 4.6 6.1 - - + -
445A TYR 3.0 18.3 + - - +
446A SER* 4.0 4.5 - - - +
448A ILE* 1.3 77.8 - - - +
450A ALA* 1.3 61.8 + - - +
452A THR* 3.1 12.3 + - + -
453A LEU* 3.0 43.4 + - + +
21B LEU* 5.6 1.1 - - + -
25B LEU* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A SER 3.2 17.4 + - - +
447A ALA* 4.2 8.7 - - - +
448A ILE 3.2 0.8 - - - -
449A LEU* 1.3 79.6 - - - +
451A ARG* 1.3 56.8 + - + +
453A LEU* 3.2 8.3 + - - +
454A ALA* 2.9 29.0 + - - +
22B ILE* 4.2 20.7 - - + +
25B LEU* 4.0 20.4 - - + +
26B LEU* 4.4 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 3.5 37.6 + - - +
277A GLN* 2.7 31.6 + - - +
278A ASP* 3.5 35.1 + - - -
447A ALA 3.2 17.4 + - - +
448A ILE* 3.2 9.2 + - - +
450A ALA* 1.3 75.6 - - + +
452A THR* 1.3 57.0 + - - +
454A ALA* 3.7 8.9 - - - +
455A LYS* 3.3 30.1 + - - +
26B LEU* 6.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO* 6.0 1.0 - - - +
111A GLU* 4.7 7.6 + - - +
120A ARG* 3.3 36.3 + - - +
448A ILE* 3.2 17.9 + - - +
449A LEU* 3.1 17.2 + - + +
450A ALA 3.0 0.2 - - - -
451A ARG* 1.3 75.2 - - - +
453A LEU* 1.3 60.6 + - + +
454A ALA 3.2 1.6 - - - -
455A LYS* 3.4 6.7 + - - +
456A GLN* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLN* 4.1 21.5 - - + +
120A ARG* 4.1 25.4 - - - -
449A LEU* 3.0 35.8 + - + +
450A ALA 3.2 2.0 + - - +
452A THR* 1.3 76.8 - - + +
454A ALA* 1.3 59.1 + - - +
456A GLN* 3.5 20.1 + - - +
457A GLU* 3.6 14.0 + - - +
18B ARG* 4.0 15.1 - - + +
21B LEU* 4.3 28.9 - - + -
22B ILE* 3.4 33.8 - - + +
25B LEU* 4.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A ALA 2.9 16.5 + - - +
451A ARG* 3.8 10.3 - - - +
452A THR 3.2 0.4 - - - -
453A LEU* 1.3 77.2 - - - +
455A LYS* 1.3 58.8 + - - +
457A GLU* 4.6 1.9 - - - +
458A ALA* 3.1 27.0 + - - +
22B ILE* 3.9 17.3 - - + -
----------------------------------------------------------
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