Contacts of the helix formed by residues 337 - 347 (chain H) in PDB entry 3LUE
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 TYR 337 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H LYS* 3.9 22.4 - - + -
26H ALA* 5.6 4.7 - - + -
27H PRO* 4.0 30.7 - - + -
30H VAL* 3.4 23.1 - - + +
334H GLU* 2.8 4.3 + - + +
336H LYS* 1.3 119.6 + - + +
338H SER* 1.3 61.8 + - - -
339H VAL 3.4 2.2 - - - -
340H TRP* 3.1 15.5 + - + +
341H ILE* 3.1 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 338 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H LEU 3.9 2.3 - - - +
141H SER* 3.6 31.0 + - - -
144H ALA* 4.1 6.9 - - - +
300H SER* 5.0 1.5 - - - -
332H PRO* 5.2 5.7 - - - +
334H GLU* 3.7 12.4 + - - +
335H ARG* 4.0 18.0 - - - -
336H LYS 3.7 1.6 + - - -
337H TYR* 1.3 73.1 - - - +
339H VAL* 1.3 65.7 + - - +
340H TRP 3.1 0.7 + - - -
341H ILE* 4.4 3.8 - - - +
342H GLY* 3.0 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ASP* 3.4 33.2 - - - +
106H THR* 4.0 9.6 - - + -
137H GLN* 3.4 45.1 - - + +
140H LEU* 3.3 22.9 - - + +
141H SER* 3.2 22.2 - - - +
154H ASP* 4.4 1.8 - - - +
301H GLY* 5.0 13.0 - - - +
335H ARG 5.4 1.3 + - - +
336H LYS 5.4 0.4 + - - -
337H TYR 3.3 1.2 + - - -
338H SER* 1.3 74.2 - - - +
340H TRP* 1.3 64.4 + - - +
342H GLY 3.5 0.2 + - - -
343H GLY 3.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 340 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 3.2 36.3 + - + +
11H ASP* 4.1 11.3 + - + +
18H LYS* 3.3 43.3 - - + -
19H ALA 3.7 0.6 - - - -
20H GLY* 3.4 33.1 - - - +
21H PHE 3.8 10.5 - - - -
24H ASP* 3.2 29.4 - - + -
25H ASP 3.8 1.8 - - - -
26H ALA* 3.4 25.4 - - - -
27H PRO* 3.4 27.6 - - + -
106H THR* 6.2 0.2 - - - -
337H TYR* 3.1 11.2 + - - +
339H VAL* 1.3 79.7 - - - +
341H ILE* 1.3 60.5 + - + +
343H GLY* 3.3 1.0 + - - -
344H SER* 3.0 38.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H ASP 4.4 6.3 - - - +
25H ASP 3.2 27.4 - - - +
26H ALA* 4.8 1.3 - - + -
27H PRO* 5.1 1.1 - - + -
144H ALA* 4.0 7.0 - - + -
337H TYR* 3.1 42.4 + - + +
338H SER* 3.1 3.3 + - - +
340H TRP* 1.3 87.5 - - + +
342H GLY* 1.3 60.7 + - - +
344H SER* 4.0 2.5 - - - -
345H ILE* 3.2 22.1 + - + +
99Q MET* 4.4 7.4 - - + -
101Q PHE* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 342 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H LEU* 3.1 32.3 - - - +
143H TYR* 4.6 5.9 - - - +
144H ALA* 3.4 13.8 - - - +
338H SER 3.0 10.7 + - - -
341H ILE* 1.3 79.6 - - - +
343H GLY* 1.3 56.2 + - - +
345H ILE* 3.8 4.0 - - - +
346H LEU* 3.2 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 343 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 3.8 14.8 - - - -
104H LEU* 4.1 6.2 - - - +
140H LEU* 3.6 22.0 - - - +
339H VAL 3.4 5.9 + - - -
340H TRP 3.3 5.6 + - - -
342H GLY* 1.3 73.7 - - - +
344H SER* 1.3 59.2 + - - +
345H ILE 3.2 0.2 + - - -
346H LEU* 3.3 3.9 + - - -
347H ALA* 2.8 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 344 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 3.4 15.2 - - - +
21H PHE 3.8 0.2 + - - -
22H ALA* 3.7 5.3 - - - +
23H GLY* 3.1 11.6 + - - -
24H ASP 2.7 41.9 + - - -
340H TRP* 3.0 32.8 + - - -
341H ILE* 3.9 6.0 - - - +
343H GLY* 1.3 74.2 - - - +
345H ILE* 1.3 48.7 + - - +
348H SER* 2.8 23.9 + - - -
101Q PHE* 5.5 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 345 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H TYR* 4.0 22.7 - - + +
144H ALA* 4.0 22.2 - - - +
341H ILE 3.2 14.3 + - - +
342H GLY* 3.8 4.5 - - - +
343H GLY 3.2 0.8 - - - -
344H SER* 1.3 71.5 - - - +
346H LEU* 1.3 68.8 - - - +
348H SER* 2.6 20.1 + - - -
349H LEU* 3.2 21.2 - - + +
101Q PHE* 1.9 95.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F GLN* 5.0 8.5 - - + -
104H LEU* 3.5 22.4 - - + -
133H TYR* 5.1 4.5 - - + -
135H ALA* 5.3 4.9 - - + -
140H LEU* 5.7 4.5 - - + -
143H TYR* 4.7 22.9 - - + -
342H GLY 3.2 16.2 - - - +
343H GLY* 3.6 4.3 - - - +
345H ILE* 1.3 82.3 - - + +
347H ALA* 1.3 56.0 + - - +
348H SER 2.8 7.8 + - - -
349H LEU* 3.0 29.4 + - + +
351H THR* 6.0 1.1 - - + -
352H PHE* 3.3 51.7 - - + +
355H MET* 4.8 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 347 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ALA* 5.8 0.3 - - - -
7H ALA* 3.9 22.8 + - + +
9H VAL* 4.8 2.5 - - + -
22H ALA* 3.6 21.5 - - + +
104H LEU* 4.4 13.2 - - + -
343H GLY 2.8 20.2 + - - +
346H LEU* 1.3 70.1 - - - +
348H SER* 1.3 55.4 + - - +
349H LEU 3.6 1.0 - - - +
352H PHE* 3.7 18.1 - - + +
356H TRP* 4.1 14.1 - - + -
----------------------------------------------------------
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